Changeset 89 for trunk/src

Timestamp:

May 20, 2010, 1:48:25 AM (15 years ago)

Author:

sommeria

Message:

many bug corrections and cleaning. Activation of the BW option in uvmat. Improvement of the interaction of get_field with uvmat.

Location:

trunk/src

Files:

• calc_field.m (modified) (1 diff)
• cell2tab.m (modified) (1 diff)
• check_field_structure.m (modified) (2 diffs)
• check_functions.m (modified) (2 diffs)
• civ.m (modified) (8 diffs)
• create_grid.m (modified) (2 diffs)
• dataview.m (modified) (1 diff)
• delete_object.m (modified) (1 diff)
• editxml.m (modified) (1 diff)
• find_field_indices.m (modified) (3 diffs)
• get_field.m (modified) (19 diffs)
• get_field/FFT.m (modified) (1 diff)
• get_field/PLOT.m (modified) (1 diff)
• imadoc2struct.m (modified) (2 diffs)
• mouse_up.m (modified) (3 diffs)
• name_generator.m (modified) (8 diffs)
• nc2struct.m (modified) (1 diff)
• plot_field.m (modified) (26 diffs)
• read_get_field.m (modified) (1 diff)
• series.fig (modified) (previous)
• series.m (modified) (24 diffs)
• series/merge_proj.m (modified) (8 diffs)
• series/sub_background.m (modified) (5 diffs)
• stra2num.m (modified) (1 diff)
• sub_field.m (modified) (1 diff)
• uvmat.fig (modified) (previous)
• uvmat.m (modified) (48 diffs)

trunk/src/calc_field.m

@@ -1 +1 @@
 %'calc_field': defines fields (velocity, vort, div...) from civx data and calculate them  
 %---------------------------------------------------------------------
-
 %
 % OUTPUT: 
 % Scal: matlab vector representing the scalar values (length nbvec defined by var_read)  
-            % if no input , Scal=list of programmed scalar names (to put in menus)
-            % if only the sclar name is put as input, vec_A=type of scalar, which can be:
+%      if no input , Scal=list of programmed scalar names (to put in menus)
+%      if only the sclar name is put as input, vec_A=type of scalar, which can be:
 %                   'vel': scalar calculated solely from velocity components
 %                   'der': needs spatial derivatives     
 %                   'var': the scalar name directly corresponds to a field name in the netcdf files
 % error: error flag
-            % error = 0; OK
-            % error = 1; the prescribed scalar cannot be read or calculated from available fields
+%      error = 0; OK
+%      error = 1; the prescribed scalar cannot be read or calculated from available fields
+%
 % INPUT:
 % ScalName: string representing the name of the scalar
 % DataIn: structure representing the field, as defined in check_field_srtructure.m
-
+%
 % FUNCTION related
 % varname_generator.m: determines the field names to read in the netcdf file, depending on the scalar

trunk/src/cell2tab.m

@@ -1 +1 @@
 %'cell2tab': transform a Matlab cell in a character array suitable for display in a table
+%------------------------------------------------------------------------
+% function Tabchar=cell2tab(Tabcell,separator) 
+%
+% OUTPUT:
+% Tabchar: character array suitable for table display
+%
 % INPUT:
-% Tabcell: (nx,ny) cell table, for nx lines
-% separator: character used for separating displayed columns
+% Tabcell: (nx,ny) cell table, for nx lines separator: character used for separating displayed columns
+
 function Tabchar=cell2tab(Tabcell,separator) 
 Tabchar={};%default

trunk/src/check_field_structure.m

@@ -1 +1 @@
 %'check_field_structure': check the validity of the field struture representation consistant with the netcdf format
-%----------------------------------------------------------------------
+%------------------------------------------------------------------------
 % function [DataOut,errormsg]=check_field_structure(Data)
 %
 % OUTPUT:
-%  Data: structure reproducing the input structure Data, with the additional elements:
+% DataOut: structure reproducing the input structure Data, with the additional elements:
 %           with fields:
 %
@@ -13 +13 @@
 % errormsg: error message which is not empty when the input structure does not have the right form
 %
-%INPUT:
+% INPUT:
 % Data:   structure containing 
 %         (optional) .ListGlobalAttribute: cell listing the names of the global attributes

trunk/src/check_functions.m

@@ -1 +1 @@
 %'check_functions': check the path and modification date for all the
-%  function in the toolbox UVMAT. Called at the opening of uvmat.fig
+%  function in the toolbox UVMAT. Called at the opening of uvmat
 %----------------------------------------------------------------------
 % function [errormsg,date_str]=check_functions
@@ -7 +7 @@
 % errormsg: error message listing functions whose paths are not in the directory of uvmat.m
 % date_str: date of the most recent modification of a file in the toolbox
-%
+
 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 %  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.

trunk/src/civ.m

@@ -181 +181 @@
 
 % set the range of fields (1:1 by default) and selected pair
-if isempty(num2)||isequal(num2,num1)
+if isnan(num2)||isequal(num2,num1)
     num_ref_i=num1;
 else
@@ -188 +188 @@
     browse.incr_pair(2)=0;
 end
-if isempty(num_b)||isequal(num_a,num_b)
-    if isempty(num_a)
+if isnan(num_b)||isequal(num_a,num_b)
+    if isnan(num_a)
         num_ref_j=1;
     else
@@ -291 +291 @@
 [RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
 filebase=fullfile(RootPath,RootFile);
-num_i1=stra2num(str1);
-if isempty(num_i1),num_i1=1;end
-num_i2=stra2num(str2);
-if isempty(num_i2),num_i2=num_i1;end
+num_i1=str2double(str1);
+if isnan(num_i1),num_i1=1;end
+num_i2=str2double(str2);
+if isnan(num_i2),num_i2=num_i1;end
 num_j1=stra2num(str_a);
-if isempty(num_j1),num_j1=1;end
+if isnan(num_j1),num_j1=1;end
 num_j2=stra2num(str_b);
-if isempty(num_j2),num_j2=num_j1;end 
+if isnan(num_j2),num_j2=num_j1;end 
 if isequal(get(handles.compare,'Value'),1)
     browse=[];%initialisation
@@ -615 +615 @@
     end
 end   
-    
 % no image documentation file found: look for a series of existing images or .nc files 
 if isempty(time) && ~isequal(ext,'.nc') && ~strcmp(nom_type_ima,'none') && ~strcmp(nom_type_ima,'') && ~strcmp(nom_type_ima,'*')
@@ -646 +645 @@
     end
     first_i=max(field_i,1);
-        %determine the set of times and possible intervals for CIV
+
+    if strcmp(nom_type_ima,'_i_j')
+        field_i=field_count;
+        field_j=1;
+        jdetect=1;
+        while jdetect==1 %look for the maximum file number in the series
+            imagename=name_generator(filebase,field_i,field_j,ext_ima,nom_type_ima);
+            jdetect=(exist(imagename,'file')==2);
+            if jdetect
+                field_j=field_j+1;
+            end
+            %SEE CASE OF NETCDF FILES
+            %             nbdetect=nbdetect+(exist(imagename,'file')==2);
+        end
+        nb_field_j=field_j-1;% last detected field number
+    end
+
+    
+    %determine the set of times and possible intervals for CIV
  %   dt=(1/1000)*str2num(get(handles.dt,'String'));
     time=[0:nb_field-1]';% time=file index -1  by default
+    if strcmp(nom_type_ima,'_i_j') 
+       % time=[0:nb_field-1]'*ones(1,nb_field_j);% time=file index -1  by default
+       time=[0:nb_field-1]'*[0:nb_field_j-1];% time=file index -1  by default
+    end
+  
+
     set(handles.mode,'String',{'series(Di)'})
 end
@@ -2662 +2685 @@
         filename_bat(end-2:end)='bat';
         fid=fopen(filename_bat,'w');
+          
         fprintf(fid,cmd);
         fclose(fid);
@@ -5152 +5176 @@
 ref.num_a=stra2num(str_a);
 ref.num_b=stra2num(str_b);
-ref.num1=str2num(field_count);
-ref.num2=str2num(str2);
+ref.num1=str2double(field_count);
+ref.num2=str2double(str2);
 browse=[];%initialisation
 if ~isequal(ref.ext,'.nc')
@@ -5248 +5272 @@
 set(handles.thresh_vel2,'String','0');
 
-%------------------------------------------------------------------------
-% transform letters to numbers
-function numres=stra2num(str)
-%------------------------------------------------------------------------
-numres=double(str)-96;
-if double(str) >= 48 & double(str) <= 57 % = 1 for numbers
-    numres=str2num(str);
-end
+% %------------------------------------------------------------------------
+% % transform letters to numbers
+% function numres=stra2num(str)
+% %------------------------------------------------------------------------
+% numres=double(str)-96;
+% if double(str) >= 48 & double(str) <= 57 % = 1 for numbers
+%     numres=str2num(str);
+% end
 
 %------------------------------------------------------------------------

trunk/src/create_grid.m

@@ -1 +1 @@
 %'create_grid': called by the GUI geometry_calib to create a physical grid 
+%------------------------------------------------------------------------
 % coord=create_grid(input_grid)
 %
@@ -5 +6 @@
 % coord: matrix (nbpoint, 3) of coordinates for grid points, with columns x,y,z
 %
-%INPUT:
+% INPUT:
 % input_grid (optional): structure to initiate the GUI with fields .x_0,.Dx,.x_1
 % (defining x coordinates), .y_0,.Dy,.y_1 (defining y coordinates)

trunk/src/dataview.m

@@ -3 +3 @@
 % function varargout = series(varargin)
 % associated with the GUI dataview.fig
-%
+
 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 %  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.

trunk/src/delete_object.m

@@ -1 +1 @@
 %'delete_object': delete a projection object, defined by its index in the Uvmat list or by its graphic handle
+%------------------------------------------------------------------------
+% function delete_object(hObject)
 %
-%INPUT:
+% INPUT:
 % hObject: object index (if integer) or handle of the graphic object. If
-% hObject is a subobject, the parent object is detected and deleted. 
+%          hObject is a subobject, the parent object is detected and deleted. 
 
 function delete_object(hObject)

trunk/src/editxml.m

@@ -6 +6 @@
 %
 %INPUT: inputfile:  name of an xml file
-%
+
 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 %  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.

trunk/src/find_field_indices.m

@@ -1 +1 @@
 %'find_file_indices': test field structure for input in proj_field and plot_field
-%group the variables  into 'fields' with common dimensions
-%----------------------------------------------------------------------
+%    group the variables  into 'fields' with common dimensions
+%------------------------------------------------------------------------
 % function [DimVarIndex,CellVarIndex,NbDim,VarType]=find_field_indices(Data)
 %
-%OUTPUT:
+% OUTPUT:
 % CellVaxIndex: cell whose elements are arrays of indices in the list data.ListVarName  
 %              CellvarIndex{i} represents a set of variables with the same dimensions
@@ -18 +18 @@
 %      .discrete: like scalar, but set of data points without continuity, represented as dots in a usual plot, instead of continuous lines otherwise
 %      .scalar: scalar field (default)
-%
+%      .coord: vector of indices of coordinate variables corresponding to matrix dimensions
 %   
-%INPUT:
+% INPUT:
 % Data: structure representing fields, output of check_field_structure
 %            .ListDimName: cell listing the names of the array dimensions
@@ -153 +153 @@
         return
     end
-    NbDim(icell)=0;% nbre of space dimensions 
-    if numel(VarIndex)>1
+    %NbDim(icell)=0;% nbre of space dimensions 
+    NbDim(icell)=numel(DimCell);
+    test_coord=0;
+    if numel(VarIndex)>1      
         if ~isempty(ivar_coord_z)
             NbDim(icell)=3;
+            test_coord=1;
         elseif ~isempty(ivar_coord_y)
             NbDim(icell)=2;
+            test_coord=1;
         elseif ~isempty(ivar_coord_x)
             NbDim(icell)=1;
+            test_coord=1;
         end
     end 
     % look at coordinates variables  
     coord=zeros(1,numel(DimCell));%default
-    if NbDim(icell)==0 && ~isempty(VarDimName)% no unstructured coordinate found 
+%     if NbDim(icell)==0 && ~isempty(VarDimName)% no unstructured coordinate found 
+    if  ~test_coord && ~isempty(VarDimName)
         for idim=1:numel(DimCell)   %loop on the dimensions of the variables in cell #icell
             for ivardim=1:numel(VarDimName)

trunk/src/get_field.m

@@ -55 +55 @@
 % Update handles structure
 guidata(hObject, handles);
-%pathuvmat=fileparts(which('uvmat'));
-%addpath(fullfile(pathuvmat,'FIELD_FCT'))
-%loads the information stored in prefdir to initiate the browser and the list of functions
+
+%ACTION menu: builtin fcts
 menu_str={'PLOT';'FFT';'filter_band';'histogram'}; %list of functions included in 'get_field.m'
-nb_builtin=numel(menu_str)-1;
-%menu_str(end)=[];%remove from the list the last option 'more...'
-path_get_field=fileparts(which('get_field'));%path of the function 'get_field'
+nb_builtin=numel(menu_str);
+path_uvmat=fileparts(which('uvmat'));%path of the function 'uvmat'
+addpath(fullfile(path_uvmat,'get_field'))
+testexist=zeros(size(menu_str'));%default
 for ilist=1:length(menu_str)
-    fct_path{ilist,1}=fullfile(path_get_field,'get_field');%paths of the fuctions buil-in in 'get_field.m'
-end
+    if exist(menu_str{ilist},'file')
+        fct_handle{ilist,1}=str2func(menu_str{ilist});
+        testexist(ilist)=1;
+    else
+        fct_handle{ilist,1}=[];
+        testexist(ilist)=0;
+    end
+end
+rmpath(fullfile(path_uvmat,'get_field'))
+
 dir_perso=prefdir;
 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
@@ -73 +81 @@
          for ilist=1:length(h.get_field_fct)
             [path,file]=fileparts(h.get_field_fct{ilist});
-            fct_path=[fct_path; {path}];%concatene the list of paths
-            menu_str=[menu_str; {file}];
+            addpath(path)        
+            if exist(file,'file')
+                h_func=str2func(file);
+                testexist=[testexist 1]; 
+             else
+                h_func=[];
+                testexist=[testexist 0]; 
+             end
+             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
+             rmpath(path)
+             menu_str=[menu_str; {file}]; 
          end
      end
 end
+menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
+fct_handle=fct_handle(testexist==1);
 menu_str=[menu_str;{'more...'}];
 set(handles.ACTION,'String',menu_str)
-set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION  
-ACTION_Callback(hObject, eventdata, handles) 
+set(handles.ACTION,'UserData',fct_handle)% store the list of path in UserData of ACTION
+set(handles.path_action,'String',fullfile(path_uvmat,'get_field'))
+set(handles.ACTION,'Value',1)% PLOT option selected
 set(hObject,'WindowButtonUpFcn',{@mouse_up_gui,handles})%set mouse click action function
 if exist('filename','var')& ischar(filename)
-    set(handles.inputfile,'String',filename)
+    set(handles.inputfile,'String',filename)% prefill the input file name 
+    set(handles.inputfile,'Enable','off')% desactivate the input file edit box   
+    set(handles.list_fig,'Value',2)% plotting axes =uvmat selected
+    set(handles.list_fig,'Visible','off')% 
+    set(handles.RUN,'Visible','off')% RUN button not visible (passive mode, get_field used to define the field for uvamt)
+    set(handles.MenuOpen,'Visible','off')
+    set(handles.MenuExport,'Visible','off')
+    set(handles.MenuHelp,'Visible','off')
     inputfile_Callback(hObject, eventdata, handles)
 else
     set(handles.inputfile,'String','')   
 end
+%ACTION_Callback(hObject, eventdata, handles) 
 if exist('Field','var') & isstruct(Field)
         Field_input(eventdata,handles,Field)
@@ -194 +222 @@
     if ~isempty(VarType{imax}.vector_x) && ~isempty(VarType{imax}.vector_y)      
         set(handles.check_vector,'Value',1)
+        set(handles.check_scalar,'Value',0)
         set(handles.vector_x,'Value',VarType{imax}.vector_x)
         set(handles.vector_y,'Value',VarType{imax}.vector_y)
-        set(handles.check_scalar,'Value',0)
+        if ~isempty(VarType{imax}.coord_x) && ~isempty(VarType{imax}.coord_y)
+            set(handles.coord_x_vectors,'Value',VarType{imax}.coord_x+1)
+            set(handles.coord_y_vectors,'Value',VarType{imax}.coord_y+1)
+        end
+        if ~isempty(VarType{imax}.coord) 
+            set(handles.coord_y_vectors,'Value',VarType{imax}.coord(1)+1)
+            if numel(VarType{imax}.coord)>=2
+                set(handles.coord_x_vectors,'Value',VarType{imax}.coord(2)+1)
+            end
+        end
     else
         set(handles.check_scalar,'Value',1)
@@ -202 +240 @@
         if isfield(VarType{imax},'scalar') && length(VarType{imax}.scalar)>=1
             set(handles.scalar,'Value',VarType{imax}.scalar(1))
+            if ~isempty(VarType{imax}.coord_x) && ~isempty(VarType{imax}.coord_y)
+                set(handles.coord_x_scalar,'Value',VarType{imax}.coord_x+1)
+                set(handles.coord_y_scalar,'Value',VarType{imax}.coord_y+1)
+            end
+            if ~isempty(VarType{imax}.coord)
+                set(handles.coord_y_scalar,'Value',VarType{imax}.coord(1)+1)
+                if numel(VarType{imax}.coord)>=2
+                    set(handles.coord_x_scalar,'Value',VarType{imax}.coord(2)+1)
+                end
+            end
         end
     end
@@ -284 +332 @@
 % update_UserData(handles)
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on selection change in scalar menu.
 function scalar_Callback(hObject, eventdata, handles)
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 Aindex=get(handles.scalar,'Value');
 Astring=get(handles.scalar,'String');
@@ -293 +341 @@
 update_field(hObject, eventdata, handles,VarName)
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on selection change in coord_x_scalar.
 function coord_x_scalar_Callback(hObject, eventdata, handles)
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 index=get(handles.coord_x_scalar,'Value');
 string=get(handles.coord_x_scalar,'String');
@@ -302 +350 @@
 update_field(hObject, eventdata, handles,VarName)
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on selection change in coord_y_scalar.
 function coord_y_scalar_Callback(hObject, eventdata, handles)
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 index=get(handles.coord_y_scalar,'Value');
 string=get(handles.coord_y_scalar,'String');
@@ -311 +359 @@
 update_field(hObject, eventdata, handles,VarName)
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on selection change in coord_z_scalar.
 function coord_z_scalar_Callback(hObject, eventdata, handles)
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 index=get(handles.coord_z_scalar,'Value');
 string=get(handles.coord_z_scalar,'String');
@@ -320 +368 @@
 update_field(hObject, eventdata, handles,VarName)
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on selection change in vector_x.
 function vector_x_Callback(hObject, eventdata, handles)
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 index=get(handles.vector_x,'Value');
 string=get(handles.vector_x,'String');
@@ -329 +377 @@
 update_field(hObject, eventdata, handles,VarName)
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on selection change in vector_y.
 function vector_y_Callback(hObject, eventdata, handles)
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 index=get(handles.vector_y,'Value');
 string=get(handles.vector_y,'String');
@@ -338 +386 @@
 update_field(hObject, eventdata, handles,VarName)
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on selection change in vector_z.
 function vector_z_Callback(hObject, eventdata, handles)
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 index=get(handles.vector_z,'Value');
 string=get(handles.vector_z,'String');
@@ -347 +395 @@
 update_field(hObject, eventdata, handles,VarName)
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on selection change in coord_x_vectors.
 function coord_x_vectors_Callback(hObject, eventdata, handles)
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 index=get(handles.coord_x_vectors,'Value');
 string=get(handles.coord_x_vectors,'String');
@@ -736 +784 @@
 function RUN_Callback(hObject, eventdata, handles)
 %---------------------------------------------------------
-path_get_field=fileparts(which('get_field'));
-list=get(handles.ACTION,'String');
+%path_get_field=fileparts(which('get_field'));
+%list=get(handles.ACTION,'String');
 index=get(handles.ACTION,'Value');
-ACTION=list{index};
-list_path=get(handles.ACTION,'UserData');
-%hselect_field=get(handles.inputfile,'parent');%handle of the get_field interface
-fct_path=list_path{index}; %path stored for the function ACTION
-if ~isequal(fct_path,path_get_field)
-%     eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
-%     if ~isequal(spath,fct_path)& exist(fct_path,'dir')
-        addpath(fct_path)% add the prescribed path if not the current one
-%     end
-end
-% fct_path
-eval(['h_fun=@' ACTION ';'])
-if ~isequal(fct_path,path_get_field)
-        rmpath(fct_path)% add the prescribed path if not the current one    
-end
-
+% ACTION=list{index};
+list_func=get(handles.ACTION,'UserData');
+h_fun=list_func{index};
+% %hselect_field=get(handles.inputfile,'parent');%handle of the get_field interface
+% fct_path=list_path{index}; %path stored for the function ACTION
+% if ~isequal(fct_path,path_get_field)
+%     addpath(fct_path)% add the prescribed path if not the current one
+% end
+% eval(['h_fun=@' ACTION ';'])
+% if ~isequal(fct_path,path_get_field)
+%      rmpath(fct_path)% add the prescribed path if not the current one    
+% end
 set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
 drawnow
-h_fun(handles.figure1);%handles.figure1 =handles of the GUI get_field
+SubField=h_fun(handles.figure1);%handles.figure1 =handles of the GUI get_field
+if ~isempty(SubField)
+    plot_get_field(SubField,handles)
+end
 browse_fig(handles.list_fig); %update the list of new existing figures
 
+%------------------------------------------------------------------------
+function plot_get_field(SubField,handles)
+%------------------------------------------------------------------------
+list_fig=get(handles.list_fig,'String');
+val=get(handles.list_fig,'Value');
+if strcmp(list_fig{val},'uvmat')
+    set(handles.figure1,'Name','uvmat_field')
+    set(handles.inputfile,'Enable','off')% desactivate the input file edit box   
+%     set(handles.list_fig,'Visible','off')% 
+    set(handles.RUN,'Visible','off')% RUN button not visible (passive mode, get_field used to define the field for uvamt)
+    set(handles.MenuOpen,'Visible','off')
+    set(handles.MenuExport,'Visible','off')
+    uvmat(get(handles.inputfile,'String'))
+else
+    hfig=str2num(list_fig{val});% chosen figure number from tyhe GUI
+    if isempty(hfig)
+        hfig=figure;
+        list_fig=[list_fig;num2str(hfig)];
+        set(handles.list_fig,'String',list_fig);
+        haxes=axes;
+    else
+        figure(hfig);
+    end
+    haxes=findobj(hfig,'Type','axes');
+    plot_field(SubField,haxes) 
+end
 
 %------------------------------------------------
@@ -1038 +1111 @@
 if isequal(val,0)
     set(handles.PanelScalar,'Visible','off')
-%      set(handles.scalar,'Visible','off')
-%     set(handles.ordinate,'Max',2.0)%allow multiple ordinate input option
-%     if isequal(get(handles.check_vector,'Value'),0);
-%         set(handles.coord_z_vectors_scalar,'Visible','off')
-%     end
 else
     set(handles.PanelScalar,'Visible','on')
-%     set(handles.scalar,'Visible','on')
-%     val=get(handles.ordinate,'Value');
-%     val=val(1);
-%     set(handles.ordinate,'Value',val);%suppress multiple ordinates
-%     set(handles.ordinate,'Max',1.0);%suppress multiple ordinate input option
-%       set(handles.coord_z_vectors_scalar,'Visible','on')
 end
 
@@ -1062 +1124 @@
     set(handles.PanelVectors,'Visible','on')
 end
-
-
 
 %-----------------------------
@@ -1088 +1148 @@
 index_ACTION=get(handles.ACTION,'Value');% selected string index
 ACTION= list_ACTION{index_ACTION}; % selected string
-path_get_field=which('get_field');%path to series.m
-list_path=get(handles.ACTION,'UserData');
-
-% nb_builtin=0;
-% if iscell(list_path)
-%     for ilist=1:length(list_path)
-%         if isequal(list_path{ilist},path_get_field)
-%             nb_builtin=nb_builtin+1;
-%         else
-%             break
-%         end
-%     end
-% end
-% if nb_builtin==0% the path to get_field has been changed, reinitialize
-%     get_field_OpeningFcn(hObject, eventdata, handles)
-%     return
-% end
-
+list_func_handles=get(handles.ACTION,'UserData');% get list of function handles (full address of the function, including name and path)
+ff=functions(list_func_handles{end});
 % add a new function to the menu
 if isequal(ACTION,'more...')
-    pathfct=fileparts(path_get_field);
-    browse_name=fullfile(path_get_field,'FIELD_FCT');
-    if length(list_path)>nb_builtin
-        browse_name=list_path{end};% initialize browser with  the path of the last introduced function
-    end
+%     pathfct=fileparts(path_get_field);
+%     browse_name=fullfile(path_get_field,'FIELD_FCT');
+%     if length(list_path)>nb_builtin
+%         browse_name=list_path{end};% initialize browser with  the path of the last introduced function
+%     end
     [FileName, PathName] = uigetfile( ...
        {'*.m', ' (*.m)';
         '*.m',  '.m files '; ...
         '*.*', 'All Files (*.*)'}, ...
-        'Pick a file',browse_name);
+        'Pick a file',ff.file);
     if length(FileName)<2
         return
@@ -1126 +1170 @@
         return
     end
-%     ACTION=FileName(1:end-2);% ACTION choice updated by the selected item  
+
     % insert the choice in the action menu
    menu_str=update_menu(handles.ACTION,ACTION);%new action menu in which the new item has been appended if needed
    index_ACTION=get(handles.ACTION,'Value');% currently selected index in the list
-   list_path{index_ACTION}=PathName;
+   addpath(PathName)
+   list_func_handles{index_ACTION}=str2func(ACTION);% create the function handle corresponding to the newly seleced function
+   set(handles.ACTION,'UserData',list_func_handles)
+   set(handles.path_action,'enable','inactive')% indicate that the current path is accessible (not 'off')
+   %list_path{index_ACTION}=PathName;
    if length(menu_str)>nb_builtin+5;
        nbremove=length(menu_str)-nb_builtin-5;
        menu_str(nb_builtin+1:end-5)=[];
-       list_path(nb_builtin+1:end-4)=[];
+       list_func_handles(nb_builtin+1:end-4)=[];
        index_ACTION=index_ACTION-nbremove;
        set(handles.ACTION,'Value',index_ACTION)
        set(handles.ACTION,'String',menu_str)
-   end
-   list_path{index_ACTION}=PathName;
-   set(handles.ACTION,'UserData',list_path);
-   set(handles.path_action,'enable','inactive')% indicate that the current path is accessible (not 'off')
-   
+   end   
    %record the current menu in personal file profil_perso
    dir_perso=prefdir;
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    for ilist=nb_builtin+1:length(menu_str)-1
-       get_field_fct{ilist-nb_builtin}=fullfile(list_path{ilist},[menu_str{ilist} '.m']);
+       ff=functions(list_func_handles{ilist});
+       get_field_fct{ilist-nb_builtin}=ff.file;
    end
    if exist(profil_perso,'file')
@@ -1163 +1208 @@
 end
 
-   %check the current path to the selected function
-PathName=list_path{index_ACTION};%current recorded path
-% if ~isequal(path_get_field,PathName)
-%     CurrentPath=fileparts(which(ACTION));
-%     if ~isequal(CurrentPath,PathName)%&&~isequal(CurrentPath,fullfile(PathName,'private'))
-%         addpath(PathName) 
-%         errormsg=check_functions;
-%         msgbox_uvmat('CONFIRMATION',[['path ' PathName ' added to the current Matlab pathes'];errormsg])
-%     end
-% end
-set(handles.path_action,'String',PathName); %show the path to the senlected function 
-    
-    
-%     fct_name=fullfile(PathName, FileName);
-%     if ~exist(fct_name,'file')
-%            msgbox_uvmat('ERROR',['procesing fct ' fct_name ' not found'])
-%     else
-%        ACTION=FileName(1:end-2);% 
-%        menu=update_menu(handles.ACTION,ACTION);%add the selected fct to the menu
-%        index_ACTION=get(handles.ACTION,'Value');% selected string index
-%        list_path{index_ACTION}=PathName;
-%        set(handles.ACTION,'UserData',list_path)
-%        if exist(profil_perso,'file')
-%             save (profil_perso,'coord_fct','-append'); %store the root name for future opening of uvmat
-%         end
-%     end   
-%     
-%     
-%     fileinput=FileName;%complete file name 
-%     eval(['spath=which(''' FileName ''');'])% current path to the function FileName
-%     if ~isequal(spath,PathName)
-%         addpath(PathName)
-%     end
-%     FileName([end-1:end])=[];
-%     
-%    % insert the choice in the action menu
-%     nbACTION=length(list_ACTION);
-%     index=0;
-%     for ilist=1:nbACTION
-%        if isequal(FileName,list_ACTION{ilist})%look for the selected scalar in the fields_input menu
-%             index=ilist;% 
-%        end
-%     end
-%     if index==0
-%        list_ACTION{nbACTION}=FileName; %put the chosen fct at the penultimate place in the fields_input menu
-%        list_path{nbACTION}=PathName;
-%        index=nbACTION;
-%        list_ACTION{nbACTION+1}='more...';
-%        set(handles.ACTION,'String',list_ACTION)
-%     end
-%     set(handles.ACTION,'Value',index);% store the selected scalar type
-%     set(handles.ACTION,'UserData',list_path);
-%     usr_defined_fct=fct_name;
-%     nbmenu=length(list_ACTION);
-%     nbadd=nbmenu-5;
-%     ilist=0;
-%     for imenu=nbmenu-min(4,nbadd):nbmenu-1
-%       ilist=ilist+1;
-%       fct_get_field{ilist,1}=list_ACTION{imenu};
-%       fct_path_get_field{ilist}=list_path{imenu};
-%     end
-%     if exist(profil_perso,'file')
-%         save(profil_perso,'usr_defined_fct','fct_get_field','fct_path_get_field','-append')
-%     else
-%        save(profil_perso,'usr_defined_fct','fct_get_field','fct_path_get_field','-V6')
-%     end
-% end
-
-% %check the current path to the selected function
-% list_path
-% PathName=list_path{index_ACTION}
-% CurrentPath=fileparts(which(ACTION))
-% if ~isequal(PathName,CurrentPath)
-%     addpath(PathName) 
-%     errormsg=check_functions;
-%     msgbox_uvmat('WARNING',[['path ' PathName ' added to the current Matlab pathes'];errormsg])
-% end
-% set(handles.path_action,'String',fullfile(PathName,' ')); %show the path to the senlected function
-
-%default setting for the visibility of the GUI elements*
-if ~isequal(ACTION,'PLOT')
-    varargout=feval(ACTION);% input list asked by the selected function
-    test_1Dplot=[];
-    test_scalar=[];
-    test_vector=[];
-    for ilist=1:length(varargout)
-        switch varargout{ilist,1}
+%check the current path to the selected function
+h_fun=list_func_handles{index_ACTION};
+if isa(h_fun,'function_handle')
+    func=functions(h_fun);
+    set(handles.path_action,'String',fileparts(func.file)); %show the path to the senlected function
+    GUI_input=h_fun();%handles.figure1 =handles of the GUI get_field
+else
+    set(handles.path_action,'String','')
+    msgbox_uvmat('ERROR','unknown path to ACTION function, reload it')
+    return
+end
+
+%prepare the GUI options for the selected ACTION
+test_1Dplot=0;
+test_scalar=0;
+test_vector=0;
+if iscell(GUI_input)
+    for ilist=1:length(GUI_input)
+        switch GUI_input{ilist}
                            %RootFile always visible
             case 'check_1Dplot'   
-                 test_1Dplot=isequal(lower(varargout{ilist,2}),'y');
+                 test_1Dplot=1;
             case 'check_scalar'
-                 test_scalar=isequal(lower(varargout{ilist,2}),'y');   
+                 test_scalar=1;   
             case 'check_vector'   
-                 test_vector=isequal(lower(varargout{ilist,2}),'y'); 
+                 test_vector=1; 
         end
     end
-    if test_1Dplot==0
-        set(handles.check_1Dplot,'Value',0);
-    end
-    if test_1Dplot==1
-        set(handles.check_1Dplot,'Value',1);
-    end
-    if test_scalar==0
-        set(handles.check_scalar,'Value',0); 
-    end
-    if test_scalar==1
-        set(handles.check_scalar,'Value',1); 
-    end
-    if test_vector==0
-        set(handles.check_vector,'Value',0);
-    end
-    if test_vector==1
-        set(handles.check_vector,'Value',1);
-    end
-    check_1Dplot_Callback(hObject, eventdata, handles)
-    check_scalar_Callback(hObject, eventdata, handles)
-    check_vector_Callback(hObject, eventdata, handles)
-end
+end
+set(handles.check_1Dplot,'Value',test_1Dplot);
+set(handles.check_scalar,'Value',test_scalar); 
+set(handles.check_vector,'Value',test_vector);
+check_1Dplot_Callback(hObject, eventdata, handles)
+check_scalar_Callback(hObject, eventdata, handles)
+check_vector_Callback(hObject, eventdata, handles)
+
 
 %-----------------------------------------------------
@@ -1463 +1426 @@
 end
 
-% %store input file in personal file uvmat_perso.mat
-% dir_perso=prefdir;
-% profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
-% if exist(profil_perso,'file')
-%     save (profil_perso,'RootPath','SubDir','RootFile','NomType', 'ext','-append'); %store the root name for future opening of uvmat
-% else
-%    save (profil_perso,'RootPath','SubDir','RootFile','NomType', 'ext'); %store the root name for future opening of uvmat 
-% end   
-
-
 % --------------------------------------------------------------------
 function MenuFile_1_Callback(hObject, eventdata, handles)

trunk/src/get_field/FFT.m

@@ -3 +3 @@
 %requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
 if ~exist('hget_field','var')
-    GUI_input={'check_1Dplot','y';...%
-        'check_scalar','n';... % 
-        'check_vector','n'... %
-               };
+    GUI_input={'check_1Dplot'};
     return %exit the function 
 end

trunk/src/get_field/PLOT.m

@@ -1 +1 @@
 %---------------------------------------------------------
 % --- Executes on button press in RUN.
-function PLOT(hget_field)
+function SubField=PLOT(hget_field)
 %---------------------------------------------------------
+SubField=[]; %default
+if ~exist('hget_field','var')
+    return
+end
 [SubField,errormsg]=read_get_field(hget_field);
 if ~isempty(errormsg)
     msgbox_uvmat('ERROR',['error in read_get_field/PLOT input:' errormsg])
-    return
 end
-handles=guidata(hget_field);
-list_fig=get(handles.list_fig,'String');
-val=get(handles.list_fig,'Value');
-if strcmp(list_fig{val},'uvmat')
-    uvmat(SubField)
-else
-    hfig=str2num(list_fig{val});% chosen figure number from tyhe GUI
-    if isempty(hfig)
-        hfig=figure;
-        list_fig=[list_fig;num2str(hfig)];
-        set(handles.list_fig,'String',list_fig);
-        haxes=axes;
-    else
-        figure(hfig);
-    end
-    haxes=findobj(hfig,'Type','axes');
-    plot_field(SubField,haxes) 
-end

trunk/src/imadoc2struct.m

@@ -1 +1 @@
 %'imadoc2struct': reads the xml file for image documentation 
+%------------------------------------------------------------------------
+% function [s,errormsg]=imadoc2struct(ImaDoc) 
 %
-%function [s,errormsg]=imadoc2struct(ImaDoc) 
-%--------------------------------------------------------
 % OUTPUT:
 % s: structure representing ImaDoc
@@ -13 +13 @@
 % INPUT:
 % ImaDoc: full name of the xml input file with head key ImaDoc
-%function [s,error,Heading,nom_type_ima,ext_ima,abs_time,TimeUnit,mode,NbSlice]=imadoc2struct(ImaDoc) 
+
 function [s,errormsg]=imadoc2struct(ImaDoc) 
 

trunk/src/mouse_up.m

@@ -1 +1 @@
 %'mouse_up': function  activated when the mouse button is released
-%----------------------------------------------------------------
+%------------------------------------------------------------------------
 % function mouse_up(hObject,eventdata,handles)
 % activated by the command:
 % set(hObject,'WindowButtonUpFcn',{'mouse_up'}), 
 % where hObject is the handle of the figure
-%
-%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
+%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 %  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
-%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 %     This file is part of the toolbox UVMAT.
 % 
@@ -20 +20 @@
 %     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 %     GNU General Public License (file UVMAT/COPYING.txt) for more details.
-%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 
 function mouse_up(hObject,eventdata,handles)
@@ -344 +344 @@
     end
     if ((nbselect==0) && isequal(get(currentobj,'Type'),'axes')) || isequal(currentobj,huvmat)
-        global CurData
-        CurData=get(currentobj,'UserData');
+        global Data_uvmat
+        Data_uvmat=get(currentobj,'UserData');
         %plot_text(CurData)
         %get_field([],CurData);
-        evalin('base','global CurData')%make CurData global in the workspace
+        evalin('base','global Data_uvmat')%make CurData global in the workspace
         objtype=get(currentobj,'Type');
         display(['UserData of ' objtype ':'])
-        evalin('base','CurData') %display CurData in the workspace
+        evalin('base','Data_uvmat') %display CurData in the workspace
         commandwindow %brings the Matlab command window to the front
     end

trunk/src/name_generator.m

@@ -1 +1 @@
 %'name_generator': creates a file name from a root name and indices. 
-%---------------------------------------------------------------------
+%------------------------------------------------------------------------
 % [filename,idetect,num_i1_out,num_j1_out,num_i2_out,num_j2_out,subdir_out]=...
 %        name_generator(filebase,num_i1,num_j1,ext,nom_type,comp_input,num_i2,num_j2,subdir);
-%---------------------------------------------------------------------           
+%------------------------------------------------------------------------           
 % This function detects the existence the constructed file name and it can
 % find indices according to file existence if they are not specified
 % rmq: this function is related to the reverse functions display2name and name2diplay 
-%---------------------------------------------------------------------
+%------------------------------------------------------------------------
 % OUTPUT:
 % filename: string representing the file name (including path)
@@ -13 +13 @@
 % num_i1_out,num_j1_out,num_i2_out,num_j2_out,subdir_out: index numbers and subdirectory detected 
 %            for free input (= to the corresponding input indices when comp_input=1)
-%---------------------------------------------------------------------
+%------------------------------------------------------------------------
 % INPUT:
 % 'filebase': the root name, 
@@ -22 +22 @@
 %       nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined)
 %       nom_type='*': the same  file [filebase ext] contains successive fields (ex avi movies)
+%       nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif'
 %       nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png').
+%       nom_type='_%03d', '_%04d', or '_%05d', series of indexed images with _ and numbers completed with zeros to 3, 4 or 5 digits, e.g.'aa_045.tif'
 %       nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif'
 %       nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png')
@@ -28 +30 @@
 %       nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc')
 %       nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc')
+%       nom_type='%3da','%3dA' with a numerical index and an index letter(e.g.'aa045b.png'), 
 %       nom_type='#a','#A' with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j')
-%       nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif'
-%       nom_type='_%03d', '_%04d', or '_%05d', series of indexed images with _ and numbers completed with zeros to 3, 4 or 5 digits, e.g.'aa_045.tif'
-%       nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE
-%       nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
-%       nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
+%       nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'),
+%       nom_type='%3d_ab' from pairs of '%3da' images (e.g. 'aa045bc.nc')
 %'comp_input' (for nom_type involving index pairs (e.g. netc))
 %       comp_input=1: the index pair is imposed, 
@@ -48 +48 @@
 sizf=size(filebase);
 if (~ischar(filebase)||~isequal(sizf(1),1)),filebase='';end
+if ~exist('ext','var')
+    ext='';
+end
+if ~exist('nom_type','var')
+    nom_type='';
+end
 if ~ischar(ext),ext='';end
-% filename=[filebase ext];%default
 idetect=0;
-if ~exist('num_i1','var') || isequal(num_i1,[]) 
+if ~exist('num_i1','var') || isempty(num_i1) || isnan(num_i1)
     num_i1=1; %default
 end
-if ~exist('num_j1','var') || isequal(num_j1,[]) 
+if ~exist('num_j1','var') ||  isempty(num_j1) || isnan(num_j1)
     num_j1=1; %default
 end
-if ~exist('num_i2','var') || isequal(num_i2,[]) 
+if ~exist('num_i2','var') ||  isempty(num_i2) || isnan(num_i2)
     num_i2=num_i1; %default
 end
-if ~exist('num_j2','var') || isequal(num_i2,[]) 
+if ~exist('num_j2','var') || isempty(num_j2) || isnan(num_j2)
     num_j2=num_j1; %default
 end
@@ -71 +76 @@
 num_j2_out=num_j2;%default output
 
-test_pairs=isequal(nom_type,'netc_old')| isequal(nom_type,'netc_2D') | isequal(nom_type,'netc_3D')| isequal(nom_type,'_i1-i2_j1-j2')| ...
-  isequal(nom_type,'netc_series')| isequal(nom_type,'#_ab')| isequal(nom_type,'_i_j1-j2')| isequal(nom_type,'_i1-i2_j')| isequal(nom_type,'_i1-i2');
-test_2D= isequal(nom_type,'netc_old') |isequal(nom_type,'netc_2D')|isequal(nom_type,'#_ab') |isequal(nom_type,'_i_j1-j2');
-test_3D=isequal(nom_type,'netc_3D') |isequal(nom_type,'netc_series')| isequal(nom_type,'_i1-i2_j')| isequal(nom_type,'_i1-i2');
-if isequal(nom_type,'series_i')| isequal(nom_type,'_i');
+test_pairs=strcmp(nom_type,'netc_old')| strcmp(nom_type,'netc_2D') | strcmp(nom_type,'netc_3D')| strcmp(nom_type,'_i1-i2_j1-j2')| ...
+  strcmp(nom_type,'netc_series')| strcmp(nom_type,'#_ab')| strcmp(nom_type,'_i_j1-j2')| strcmp(nom_type,'_i1-i2_j')| strcmp(nom_type,'_i1-i2');
+test_2D= strcmp(nom_type,'netc_old') |strcmp(nom_type,'netc_2D')|strcmp(nom_type,'#_ab') |strcmp(nom_type,'_i_j1-j2');
+test_3D=strcmp(nom_type,'netc_3D') |strcmp(nom_type,'netc_series')| strcmp(nom_type,'_i1-i2_j')| strcmp(nom_type,'_i1-i2');
+if strcmp(nom_type,'series_i')| strcmp(nom_type,'_i');
         filename=[filebase '_' num2str(num_i1) ext];
         num_i2_out=num_i1;
         num_j1_out=[];
         num_j2_out=[]; 
-elseif length(nom_type)==5 && isequal(nom_type(1:3),'_%0')&& isequal(nom_type(5),'d');
+elseif length(nom_type)==5 && strcmp(nom_type(1:3),'_%0')&& strcmp(nom_type(5),'d');
         filename=[filebase '_' num2str(num_i1,nom_type(2:5)) ext];
         num_i2_out=num_i1;
         num_j2_out=num_j1;
-elseif isequal(nom_type,'series_i_j')| isequal(nom_type,'_i_j')
+elseif strcmp(nom_type,'series_i_j')| strcmp(nom_type,'_i_j')
         filename=[filebase '_' num2str(num_i1) '_' num2str(num_j1) ext];
         num_i2_out=num_i1;
         num_j2_out=num_j1;
-elseif isequal(nom_type,'png_old')| isequal(nom_type,'#a')| isequal(nom_type,'#A')
+elseif strcmp(nom_type,'png_old')| strcmp(nom_type,'#a')| strcmp(nom_type,'#A')
         filename=[filebase num2str(num_i1,'%03d') num2stra(num_j1,nom_type) ext];
         num_i2_out=num_i1;
         num_j2_out=num_j1;
-elseif  length(nom_type)>=5 & isequal(nom_type(2:3),'%0') & isequal(nom_type(5),'d')  %isequal(nom_type,'_%04dA') %camera PCO Toulouse
+elseif  length(nom_type)>=5 & strcmp(nom_type(2:3),'%0') & strcmp(nom_type(5),'d')  %strcmp(nom_type,'_%04dA') %camera PCO Toulouse
         filename=[filebase nom_type(1) num2str(num_i1,nom_type(2:4)) num2stra(num_j1,nom_type) ext];
         num_i2_out=num_i1;
         num_j2_out=num_j1;   
-elseif isequal(nom_type,'raw_SMD') %suffix a, b, c without extension
+elseif strcmp(nom_type,'raw_SMD') %suffix a, b, c without extension
         filename=[filebase num2str(num_i1,'%03d') num2stra(num_j1,nom_type)];
         num_i2_out=num_i1;
         num_j2_out=num_j1;
-elseif isequal(nom_type,'ima_num')| isequal(nom_type,'#')
+elseif strcmp(nom_type,'ima_num')| strcmp(nom_type,'#')
         filename=[filebase num2str(num_i1) ext];
         num_i2_out=num_i1;
         num_j1_out=[];
         num_j2_out=[];
-elseif length(nom_type)>=4 & isequal(nom_type(1:2),'%0') & isequal(nom_type(end),'d')
+elseif length(nom_type)>=4 & strcmp(nom_type(1:2),'%0') & strcmp(nom_type(end),'d')
         filename=[filebase num2str(num_i1,nom_type) ext]; %test number with a 0 before
         num_i2_out=num_i1;
@@ -115 +120 @@
     filebasesub=filebase;
     % get the root name filebasesub for the netcdf files
-    if  ~isequal(subdir,'') && ~isequal(subdir,'?') 
+    if  ~strcmp(subdir,'') && ~strcmp(subdir,'?') 
             [Path,Name]=fileparts(filebase);
             filebasesub=fullfile(Path,subdir,Name);
     end
      %inexistant pair if num_i2=0 or num_j2=0
-%     if isequal(num_i2,0)
+%     if strcmp(num_i2,0)
 %         filename=[filebasesub '*-*_' num2str(num_i1) ext];
 %         return
 %     end
-%     if isequal(num_j2,0)
+%     if strcmp(num_j2,0)
 %         filename=[filebasesub '_' num2str(num_i1) '_*-*' ext];
 %         return
@@ -232 +237 @@
 if ~isequal(subdir,'?'), subdir_out=subdir; else, subdir_out='';end;
 
-%---------------------------------------------------------------
-% search the appropriate image pair (netcdf file) corresponding to a given
-% image number
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
+% --- search the appropriate image pair (netcdf file) corresponding to a given image number
 function [filename,num_i1,num_j1,num_i2,num_j2,idetect]=search_pair(filebasesub,num_i1,num_j1,num_i2,nom_type)
+%------------------------------------------------------------------------
 % for nom_type=netc_2D or netc_old, it searches all the pairs corresponding
 % to num_i1, and chooses the most recent file.

trunk/src/nc2struct.m

@@ -16 +16 @@
 %                    .DimValue= vlalues of dimensions (added information, not requested for field description)
 %                    .VarDimIndex= list of dimension indices (added information,
-
+%
 %INPUT:
 %     nc:      name of a netcdf file (char string) or netcdf object   

trunk/src/plot_field.m

@@ -31 +31 @@
 %    The only variable attribute used for plotting purpose is .Role which can take
 %    the values
-        %       Role = 'scalar':  (default) represents a scalar field
-        %            = 'coord_x', 'coord_y',  'coord_z': represents a separate set of
-        %                        unstructured coordinate x, y  or z
-        %            = 'vector': represents a vector field whose number of components
-        %                is given by the last dimension (called 'nb_dim')
-        %            = 'vector_x', 'vector_y', 'vector_z'  :represents the x, y or z  component of a vector  
-        %            = 'warnflag' : provides a warning flag about the quality of data in a 'Field', default=0, no warning
-        %            = 'errorflag': provides an error flag marking false data,
-        %                   default=0, no error. Different non zero values can represent different criteria of elimination.
-
-
+%       Role = 'scalar':  (default) represents a scalar field
+%            = 'coord_x', 'coord_y',  'coord_z': represents a separate set of
+%                        unstructured coordinate x, y  or z
+%            = 'vector': represents a vector field whose number of components
+%                is given by the last dimension (called 'nb_dim')
+%            = 'vector_x', 'vector_y', 'vector_z'  :represents the x, y or z  component of a vector  
+%            = 'warnflag' : provides a warning flag about the quality of data in a 'Field', default=0, no warning
+%            = 'errorflag': provides an error flag marking false data,
+%                   default=0, no error. Different non zero values can represent different criteria of elimination.
+%
+%
 %         additional elements characterizing the projection object (should not be necessary)--
 %            Data.Style : style of projection object
@@ -84 +84 @@
 % PosColorbar: if not empty, display a colorbar for B&W images
 %               imposed position of the colorbar (ex [0.821 0.471 0.019 0.445])
-%
+
 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 %  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
@@ -141 +141 @@
 if testnewfig% create a new figure and axes if the plotting axes does not exist
     hfig=figure;
-    if isfield(Data,'IndexObj')&isfield(Data,'Style')&isfield(Data,'ProjMode')
+    if isfield(Data,'IndexObj') && isfield(Data,'Style') && isfield(Data,'ProjMode')
         figname=[num2str(Data.IndexObj) '-' Data.Style];
         set(hfig,'Name',figname)
     end
-    testhandle=0;
-    if isfield(PlotParam,'text_display_1')& ishandle(PlotParam.text_display_1)
+%     testhandle=0;
+    if isfield(PlotParam,'text_display_1') && ishandle(PlotParam.text_display_1)
         set(hfig,'UserData',PlotParam)
-        testhandle=1;
+%         testhandle=1;
     end
     set(hfig,'Units','normalized')
@@ -160 +160 @@
     hstack=findobj(allchild(0),'Type','figure');%current stack order of figures in matlab
 end
-if isfield(PlotParam,'text_display_1')& ishandle(PlotParam.text_display_1)
+if isfield(PlotParam,'text_display_1') && ishandle(PlotParam.text_display_1)
     PlotParam=read_plot_param(PlotParam);   
 end
@@ -171 +171 @@
 
 % check the cells of fields :
-testnbdim=1;
+% testnbdim=1;
 [CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Data);
 
@@ -180 +180 @@
 end
 if ~isfield(Data,'NbDim') %& ~isfield(Data,'Style')%determine the space dimensionb if not defined: choose the kind of plot 
-    [Data.NbDim,imax]=max(NbDim);
+    [Data.NbDim]=max(NbDim);
 end
 if isequal(Data.NbDim,0) 
@@ -207 +207 @@
     msgbox_uvmat('ERROR','volume plot not implemented yet')
     return
-else
-    testnbdim=0;
+% else
+%     testnbdim=0;
 end
 
@@ -239 +239 @@
 function hdisplay=plot_text(FieldData,hdisplay_in)
 %-------------------------------------------------------------------
-if exist('hdisplay_in','var') & ishandle(hdisplay_in) & isequal(get(hdisplay_in,'Type'),'uicontrol')
+if exist('hdisplay_in','var') && ishandle(hdisplay_in) && isequal(get(hdisplay_in,'Type'),'uicontrol')
     hdisplay=hdisplay_in;
 else
@@ -254 +254 @@
     sizss=size(ss);
     if isnumeric(ss)
-        if sizss(1)<=1 & length(ss)<5
+        if sizss(1)<=1 && length(ss)<5
             displ{icell}=num2str(ss);
         else
@@ -263 +263 @@
     elseif iscell(ss)
         sizcell=size(ss);
-        if sizcell(1)==1 & length(sizcell)==2 %line cell
+        if sizcell(1)==1 && length(sizcell)==2 %line cell
            ssline='{''';
            for icolumn=1:sizcell(2)
                if isnumeric(ss{icolumn})
-                   if size(ss{icolumn},1)<=1 & length(ss{icolumn})<5
+                   if size(ss{icolumn},1)<=1 && length(ss{icolumn})<5
                       sscolumn=num2str(ss{icolumn});%line vector
                    else
@@ -321 +321 @@
 plotstr='hhh=plot(';
 textmean={};
-abscissa_name='';
+% abscissa_name='';
 coord_x_index=[];
 test_newplot=1;
 hh=findobj(haxes,'tag','plot_line');
-num_curve=numel(hh);
+% num_curve=numel(hh);
 icurve=0;
 for icell=1:length(CellVarIndex)
@@ -351 +351 @@
     testcoordvar=0;
     charplot_0='''-''';%default
-    if isfield(data,'ObjectProjMode')& isequal(data.ObjectProjMode,'projection')
+    if isfield(data,'ObjectProjMode')&& isequal(data.ObjectProjMode,'projection')
         charplot_0='+';
     end
@@ -374 +374 @@
         VarAttribute=data.VarAttribute;
         for ivar=1:length(VarIndex) 
-             if length(VarAttribute)>=VarIndex(ivar) & isfield(VarAttribute{VarIndex(ivar)},'long_name')
+             if length(VarAttribute)>=VarIndex(ivar) && isfield(VarAttribute{VarIndex(ivar)},'long_name')
                  plotname{VarIndex(ivar)}=VarAttribute{VarIndex(ivar)}.long_name;
              else
@@ -461 +461 @@
         else
             legend_old=get(hlegend,'String');
-            if isequal(size(legend_old,1),size(legend_str,1))&~isequal(legend_old,legend_str)
+            if isequal(size(legend_old,1),size(legend_str,1))&&~isequal(legend_old,legend_str)
                 set(hlegend,'String',[legend_old legend_str]);
             end
@@ -537 +537 @@
 y_units='';
 for icell=1:length(CellVarIndex) % length(CellVarIndex) =1 or 2 (from the calling function)
-%     VarIndex=CellVarIndex{icell};
     VarType=VarTypeCell{icell};
     ivar_X=VarType.coord_x; % defines (unique) index for the variable representing unstructured x coordinate (default =[])
@@ -564 +563 @@
             eval(['vec_U=Data.' Data.ListVarName{ivar_U} ';']) 
             eval(['vec_V=Data.' Data.ListVarName{ivar_V} ';']) 
+            'TESTplot'
+            VarType.coord
             if ~isempty(ivar_X) && ~isempty(ivar_Y)% 2D field (with unstructured coordinates or structured ones (then ivar_X and ivar_Y empty)     
                 eval(['vec_X=Data.' Data.ListVarName{ivar_X} ';']) 
@@ -614 +615 @@
             [A,AX,AY]=proj_grid(AX',AY',A',[],[],'np>256');  % interpolate on a grid  
             if isfield(Data,'VarAttribute')
-                if numel(Data.VarAttribute)>=ivar_X & isfield(Data.VarAttribute{ivar_X},'units')
+                if numel(Data.VarAttribute)>=ivar_X && isfield(Data.VarAttribute{ivar_X},'units')
                     x_units=['(' Data.VarAttribute{ivar_X}.units ')'];
                 end
-                if numel(Data.VarAttribute)>=ivar_Y & isfield(Data.VarAttribute{ivar_Y},'units')
+                if numel(Data.VarAttribute)>=ivar_Y && isfield(Data.VarAttribute{ivar_Y},'units')
                     y_units=['(' Data.VarAttribute{ivar_Y}.units ')'];
                 end
@@ -629 +630 @@
             test_interp_Y=0; %default, regularly meshed Y coordinate
             if isfield(Data,'VarAttribute')
-                if numel(Data.VarAttribute)>=VarType.coord(2) & isfield(Data.VarAttribute{VarType.coord(2)},'units')
+                if numel(Data.VarAttribute)>=VarType.coord(2) && isfield(Data.VarAttribute{VarType.coord(2)},'units')
                     x_units=['(' Data.VarAttribute{VarType.coord(2)}.units ')'];
                 end
@@ -714 +715 @@
     end
     %set the color map
+    if isfield(PlotParam.Scalar,'BW')
+        BW=PlotParam.Scalar.BW; %test for BW gray scale images
+    else
+        BW=(siz==2) && (isa(A,'uint8')|| isa(A,'uint16'));% non color images represented in gray scale by default
+    end
     if siz==2 %for black and white images
         if ~isfield(PlotParam.Scalar,'AutoScal')
@@ -729 +735 @@
             MinA=PlotParam.Scalar.MinA;  
         end; 
-        if isequal(PlotParam.Scalar.AutoScal,0)|isempty(PlotParam.Scalar.MaxA)|~isa(PlotParam.Scalar.MaxA,'double') %correct if there is no numerical data in edit box
+        if isequal(PlotParam.Scalar.AutoScal,0)||isempty(PlotParam.Scalar.MaxA)||~isa(PlotParam.Scalar.MaxA,'double') %correct if there is no numerical data in edit box
             MaxA=double(max(max(A)));
         else
@@ -756 +762 @@
             contmin=intercont*floor(min(min(B))/intercont);
             contmax=intercont*ceil(max(max(B))/intercont);
-            cont_pos_plus=[0:intercont:contmax];
-            cont_pos_min=[double(contmin):intercont:-intercont];
+            cont_pos_plus=0:intercont:contmax;
+            cont_pos_min=double(contmin):intercont:-intercont;
             cont_pos=[cont_pos_min cont_pos_plus];
             sizpx=(AX(end)-AX(1))/(np(2)-1);
             sizpy=(AY(1)-AY(end))/(np(1)-1);
             x_cont=[AX(1):sizpx:AX(end)]; % pixel x coordinates for image display 
-            y_cont=[AY(1):-sizpy:AY(end)]; % pixel x coordinates for image display
+            y_cont=AY(1):-sizpy:AY(end); % pixel x coordinates for image display
             txt=ver;%version of Matlab
             Release=txt(1).Release;
@@ -783 +789 @@
             colormap(map);
         end
-        if ~isequal(PlotParam.Scalar.Contours,1)       
+        if ~isequal(PlotParam.Scalar.Contours,1)  
             % rescale the grey levels with min and max, put a grey scale colorbar
-            if (isfield(PlotParam.Scalar,'BW')& (isequal(PlotParam.Scalar.BW,1))|isa(A,'uint8')| isa(A,'uint16'))%images
+            if BW
                 B=A;
                 vec=linspace(0,1,255);%define a linear greyscale colormap
@@ -797 +803 @@
     else %color images
         axes(haxes)
-        B=uint8(A); 
+        if BW
+            B=uint16(sum(A,3));
+        else
+            B=uint8(A);
+        end
         MinA=0;
         MaxA=255;
@@ -846 +856 @@
     test_ima=1;
     %display the colorbar code for B/W images if Poscolorbar not empty
-    if siz==2 & exist('PosColorbar','var')& ~isempty(PosColorbar)
+    if siz==2 && exist('PosColorbar','var')&& ~isempty(PosColorbar)
         if isempty(hcol)|~ishandle(hcol)
              hcol=colorbar;%create new colorbar
@@ -966 +976 @@
         dy_thresh=max(abs(diffy))/2; 
         ind_jump=find(abs(diffy) > dy_thresh); %indices with diff(vec_Y)> max/2, detect change of line
-        ind_sel=[1:ind_jump(1)];%select the first line
+        ind_sel=1:ind_jump(1);%select the first line
         for i=2:2:length(ind_jump)-1
             ind_sel=[ind_sel [ind_jump(i)+1:ind_jump(i+1)]];% select the odd lines
@@ -1191 +1201 @@
     siz=size(ind);
     if siz(2)<4%if there are less than 4 selected values (4 levels)
-        values=[-9:0.5*div:9];
+        values=-9:0.5*div:9;
         ind=find((ord*values-MaxA)<0 & (ord*values-MinA)>0);
     end

trunk/src/read_get_field.m

@@ -666 +666 @@
             end
         end
-        if empty_coord_vec_x        
-                coord_x_name=DimCell{2};
-                SubField.ListVarName=[{coord_x_name} SubField.ListVarName];
-                SubField.VarDimName=[{coord_x_name} SubField.VarDimName];  
-                if testold
-                    eval(['SubField.' coord_x_name '=linspace(Coord_2(1),Coord_2(end),npxy(2));'])
-                else
-                    eval(['SubField.' coord_x_name '=[0.5 npxy(2)-0.5];'])
-                end
+        if empty_coord_vec_x 
+            if numel(DimCell)<2  
+                errormsg='undefined x coordinate';
+                return
+            end
+            coord_x_name=DimCell{2};
+            SubField.ListVarName=[{coord_x_name} SubField.ListVarName];
+            SubField.VarDimName=[{coord_x_name} SubField.VarDimName];  
+            if testold
+                eval(['SubField.' coord_x_name '=linspace(Coord_2(1),Coord_2(end),npxy(2));'])
+            else
+                eval(['SubField.' coord_x_name '=[0.5 npxy(2)-0.5];'])
+            end
             
             if ~testold

trunk/src/series.m

@@ -430 +430 @@
 update_file(hObject, eventdata, handles,fileinput,1)
 
-% --------------------------------------------------------------------
-% refresh the GUI data after introduction of a new file series
+%------------------------------------------------------------------------
+% ---  refresh the GUI data after introduction of a new file series
 function update_file(hObject, eventdata, handles,fileinput,addtest)
-%hseries=get(handles.RootPath,'parent');  
+%------------------------------------------------------------------------  
 if ~exist(fileinput,'file')
     msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
     return
 end
-hseries=handles.figure1;
+
 % refresh input root name, indices, file extension and nomenclature
 [RootPath,RootFile,field_count,str2,str_a,str_b,FileExt,NomType,SubDir]=name2display(fileinput);
+
 %check for movie image files
 if ~isempty(FileExt)
-if ~isempty(imformats(FileExt(2:end)))
-    imainfo=imfinfo(fileinput);     
-    if length(imainfo) >1 %case of image with multiple frames
-        NomType='*';
-        [RootPath,RootFile]=fileparts(fileinput);
-    end
-end
+    if ~isempty(imformats(FileExt(2:end)))
+        imainfo=imfinfo(fileinput);
+        if length(imainfo) >1 %case of image with multiple frames
+            NomType='*';
+            [RootPath,RootFile]=fileparts(fileinput);
+        end
+    end
 end
 NcType='none';%default
@@ -467 +468 @@
 set(handles.nb_field2,'Value',1)
 if addtest
-    SeriesData=get(hseries,'UserData');
+    SeriesData=get(handles.figure1,'UserData');
     SeriesData.displ_num=[0 0 0 0;SeriesData.displ_num];
     SeriesData.CurrentInputFile_1=SeriesData.CurrentInputFile;
@@ -520 +521 @@
 set(handles.first_j,'String',num2str(ref_j))
 set(handles.last_j,'String',num2str(ref_j)); 
-%set(hseries,'UserData',SeriesData);
 
 %enable other menus and uicontrols
@@ -544 +544 @@
 FileBase=fullfile(RootPath,RootFile);
 
-% nb_field{icell,1}='?';%default 
-% nb_field2{icell,1}='?';%default 
 testima=0; %test for image input
 if isequal(lower(FileExt),'.avi') %.avi file
@@ -681 +679 @@
     [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
     time=XmlData.Time;
-    size(time)
-    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';
-    XmlData.GeometryCalib=GeometryCalib;
     if error==2, warntext=['no file ' FileBase '.civ'];
     elseif error==1, warntext='inconsistent number of fields in the .civ file';
@@ -705 +689 @@
 end
 
-if ~isempty(time)
-    siztime=size(time);
-    nb_field=siztime(1);
-    nb_field2=siztime(2);
-end   
+
+% if ~isempty(time)
+%     siztime=size(time);
+%     nb_field=siztime(1);
+%     nb_field2=siztime(2);
+% end   
 set(handles.TimeUnit,'String',TimeUnit)
+%look for max indices
+if ~strcmp(NomType,'*')
+    [num_i1,num_i2,num_j1,num_j2]=find_indexseries(fileinput);
+    nb_field=max(floor((max(num_i1)+max(num_i2))/2));
+    nb_field2=max(floor((max(num_j1)+max(num_j2))/2));
+end
 if isempty(nb_field)
     nb_field_str='?';
@@ -727 +718 @@
 set(handles.nb_field,'String',nb_field_cell);
 set(handles.nb_field2,'String',nb_field2_cell);
-set(hseries,'UserData',SeriesData);
+set(handles.figure1,'UserData',SeriesData);
 
 %number of slices
@@ -743 +734 @@
 NomType_Callback(hObject, eventdata, handles)
 
+%store the root name for future opening of uvmat
 dir_perso=prefdir;
 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
-% save(profil_perso, 'FileBase'); %store the root name for future opening of uvmat
 if exist(profil_perso,'file')
     save (profil_perso,'RootPath','SubDir','RootFile','NomType', '-append'); %store the root name for future opening of uvmat
@@ -839 +830 @@
 NomType_Callback(hObject, eventdata, handles)
 
+%------------------------------------------------------------------------
 function NomType_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 hseries=get(handles.ProjObject,'Parent');
 SeriesData=get(hseries,'UserData');
@@ -897 +890 @@
                 state_j='on';
     end
-end   
+end 
 if testpair
     mode_Callback(hObject, eventdata, handles)  
 else
     set(handles.NomType,'String',NomTypeCell)
-end
-set(handles.first_j,'Visible',state_j)
-set(handles.incr_j,'Visible',state_j)
-set(handles.last_j,'Visible',state_j)
-set(handles.nb_field2,'Visible',state_j)
+    set(handles.first_j,'Visible',state_j)
+    set(handles.incr_j,'Visible',state_j)
+    set(handles.last_j,'Visible',state_j)
+    set(handles.nb_field2,'Visible',state_j)
+end
+
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%????????????
@@ -926 +920 @@
     test_find_pair=isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2')|| isequal(NomType,'#_ab');
 end
-% displ_num=[];%default
-% first_i=str2num(get(handles.first_i,'String'));
-% last_i=str2num(get(handles.last_i,'String'));
 time=[];
 if isfield(SeriesData,'Time')
@@ -939 +930 @@
 if isequal(mode,'bursts')
     enable_i(handles,'On')
-    enable_j(handles,'Off')    
+    enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)  
 elseif  isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')
     enable_i(handles,'On')
-    enable_j(handles,'On') 
+    enable_j(handles,'On') % allow both i and j index scanning
 else
     enable_i(handles,'On')
@@ -993 +984 @@
 
 %--------------------------------------------------------------
-% determine the menu for civ1 pairs depending on existing netcdf file at the middle of
-% the field series set by first_i, incr, last_i
+% determine the menu for civ1 pairs depending on existing netcdf files 
+% with the reference indices ref_i and ref_j
 %----------------------------------------------------------------
 function find_netcpair_civ(hObject, eventdata, handles,Val)
@@ -1087 +1078 @@
                 displ_num(4,ind_exist)=0;
                 %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'});
-                [Cte,var_detect,ichoice]=nc2struct(nc,{});
+                [Cte,var_detect,ichoice]=nc2struct(filename,{});
                 if isfield(Cte,'dt2')
                     dt=Cte.dt2;
@@ -1357 +1348 @@
 end
 Series.hseries=handles.figure1; % handles to the series GUI
-% if isequal(get(handles.ParamVal,'Visible'),'on')
-%     ParamKey=get(handles.ParamKey,'String');
-%     if ischar(ParamKey)
-%         ParamKey{1}=ParamKey;
-%     end
-%     ParamString=get(handles.ParamVal,'String');
-%     if ischar(ParamString)
-%         for ilist=1:size(ParamString,1)
-%             ParamVal{ilist}=ParamString(ilist,:);
-%         end
-%     else
-%         ParamVal=ParamString;
-%     end   
-% end
 
 %read the set of field numbers
@@ -1433 +1410 @@
     %case of pairs (.nc files)
     
-    if isequal(NomType{iview},'_i_j1-j2')| isequal(NomType{iview},'_i1-i2_j')| isequal(NomType{iview},'_i1-i2')| isequal(NomType{iview},'#_ab')
+    if isequal(NomType{iview},'_i_j1-j2')|| isequal(NomType{iview},'_i1-i2_j')|| isequal(NomType{iview},'_i1-i2')|| isequal(NomType{iview},'#_ab')
         ind_shift=SeriesData.displ_num(iview,:);
         if isequal(ind_shift,[0 0 0 0]) % undefined pairs
@@ -1928 +1905 @@
         end
 
-%----------------------------------------------------
-%  determine the list of index pairs of processing file 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%------------------------------------------------------------------------
+% --- determine the list of index pairs of processing file 
 function [num_i1,num_i2,num_j1,num_j2,num_i_out,num_j_out]=find_file_indices(num_i,num_j,ind_shift,NomType,mode)
+%------------------------------------------------------------------------
 num_i1=num_i;% set of first image numbers by default
 num_i2=num_i;
@@ -1938 +1915 @@
 num_i_out=num_i;
 num_j_out=num_j;
-if isequal (NomType,'_i1-i2_j') |isequal (NomType,'_i1-i2')
+if isequal (NomType,'_i1-i2_j') || isequal (NomType,'_i1-i2')
     num_i1_line=num_i+ind_shift(3);% set of first image numbers
     num_i2_line=num_i+ind_shift(4);
@@ -2211 +2188 @@
 set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
 
-%-------------------------------------------------------------
-%generates a series of file names with reference numbers between range1 and
-%range2 with increment incr. The reference number num_ref is the image number at the middle of the
-%image pair. The set of first numbers num1 of the image pairs is also
-%given as output
-%------------------------------------------------------
+%------------------------------------------------------------------------
+% --- generates a series of file names with reference numbers between range1 and
+% --- range2 with increment incr. The reference number num_ref is the image number at the middle of the
+% --- image pair. The set of first numbers num1 of the image pairs is also
+% --- given as output
 function [num_i1,num_i2,num_j1,num_j2,nbmissing]=netseries_generator(filebase,subdir,mode,first_i,incr_i,last_i,first_j,incr_j,last_j)
+%------------------------------------------------------------------------
 [Path,Name]=fileparts(filebase);
 filebasesub=fullfile(Path,subdir,Name);
@@ -2236 +2213 @@
     dirpair=dir([filebasesub '_*-*_*.nc']);
 else
-    errordlg('option *|* not yet implemented')
+    msgbox_uvmat('ERROR','option *|* not yet implemented')
     return
 end
 if isempty(dirpair)
-        errordlg('no pair detected in the selected range')
+        msgbox_uvmat('ERROR','no pair detected in the selected range')
         return
 end
-    %ind0_i=first_i:incr_i:last_i;
-    %nbcolumn=length(ind0_i);
-    %dirpair=dir([filebasesub '_*_*-*.nc']);
-if isequal(mode,'bursts')|isequal(mode,'#_ab')
+
+if isequal(mode,'bursts')||isequal(mode,'#_ab')
     icount=0;
     for ifile=1:length(dirpair)
         [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
-        
-%         if isempty(str2num(str_1))
-%             dirpair(ifile).name
-%         end
         num1_r=str2num(str_1);
         if isequal(RootFile,Name) & ~isempty(num1_r)   
@@ -2259 +2230 @@
             num_a(ifile)=stra2num(str_a);
             num_b(ifile)=stra2num(str_b);
-%             icount=icount+1;
         end      
     end
-    length(dirpair)
-%     num_j=floor((num_a+num_b)/2); %list of reference indices of the detected files
     test_range= (num_i1 >=first_i)&(num_i1<= last_i);% =1 when both numbers are in the range
     ind_i=((num_i1-first_i)/incr_i)+1;%indices i in the list of prescribed file indices 
@@ -2309 +2277 @@
     num_i1_r=num_i1_r(select);
     num_i2_r=num_i2_r(select);
-%     num_j=num_j(select);
     dirpair=dirpair(select);
     [ind_remove]=find_pairs(dirpair,ind_ij,nbcolumn*nbline) ;
@@ -2325 +2292 @@
     nbmissing=nbline*nbcolumn-length(ind_ij);
 elseif isequal(mode,'series(Dj)')
- %   ind0_i=first_i:incr_i:last_i;
- %   nbcolumn=length(ind0_i);
- %   ind0_j=first_j:incr_j:last_j;
-  %  nbline=length(ind0_j);
-  %  dirpair=dir([filebasesub '_*_*-*.nc']);
     for ifile=1:length(dirpair)
         [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
@@ -2362 +2324 @@
     num_i2=num_i1;
     nbmissing=nbline*nbcolumn-length(ind_ij);
-%     for i=1:length(indsel);%A SUPPRIMER ULTERIEUREMENT
-%         if indsel(i)==0
-%             filecell{i}='';
-%         else
-%             Name=dirpair(indsel(i)).name;
-%             filecell{i}=fullfile(Path,subdir,Name);
-%         end
-%     end
-%else
-%    errordlg('option *|* not yet implemented')
-%    return
-end
-
-function path_transform_Callback(hObject, eventdata, handles)
-% hObject    handle to path_transform (see GCBO)
-% eventdata  reserved - to be defined in a future version of MATLAB
-% handles    structure with handles and user data (see GUIDATA)
-
-% Hints: get(hObject,'String') returns contents of path_transform as text
-%        str2double(get(hObject,'String')) returns contents of path_transform as a double
-
-
-% --- Executes during object creation, after setting all properties.
-function path_transform_CreateFcn(hObject, eventdata, handles)
-% hObject    handle to path_transform (see GCBO)
-% eventdata  reserved - to be defined in a future version of MATLAB
-% handles    empty - handles not created until after all CreateFcns called
-
-% Hint: edit controls usually have a white background on Windows.
-%       See ISPC and COMPUTER.
-if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
-    set(hObject,'BackgroundColor','white');
-end
-
-
+end
+
+%------------------------------------------------------------------------
+% --- generates series of file indices corresponding to a file fileinput
+function [num_i1,num_i2,num_j1,num_j2]=find_indexseries(fileinput)
+%------------------------------------------------------------------------
+num_i1=NaN;%default
+num_i2=NaN;%default
+num_j1=NaN;%default
+num_j2=NaN;%default
+% refresh input root name, indices, file extension and nomenclature
+[RootPath,RootFile,field_count,str2,str_a,str_b,FileExt,NomType,SubDir]=name2display(fileinput);
+if strcmp(SubDir,'')
+    filebasesub=fullfile(RootPath,RootFile);
+else
+    filebasesub=fullfile(RootPath,SubDir,RootFile);
+end
+dirpair=[]; %default
+switch NomType
+    case '_i'
+        dirpair=dir([filebasesub '_*' FileExt]);
+    case '_i_j'
+        dirpair=dir([filebasesub '_*_*' FileExt]);
+    case '_i1-i2'
+        dirpair=dir([filebasesub '_*-*' FileExt]);
+    case '#_ab'
+        dirpair=dir([filebasesub '*_*' FileExt]);
+    case '_i_j1-j2'
+        dirpair=dir([filebasesub '*_*-*' FileExt]);   
+    case '_i1-i2_j'
+        dirpair=dir([filebasesub '*-*_*' FileExt]);   
+end
+%       nom_type='#' series of indexed images wich is not series_i
+%       [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif'
+%       nom_type='#a','#A' with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j')
+%       nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif'
+%       nom_type='_%03d', '_%04d', or '_%05d', series of indexed images with _ and numbers completed with zeros to 3, 4 or 5 digits, e.g.'aa_045.tif'
+%       nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE
+%       nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
+%       nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
+for ifile=1:length(dirpair)
+    [RootPath,RF,str_1,str_2,str_a,str_b]=name2display(dirpair(ifile).name);
+    num_i1(ifile)=str2double(str_1);
+    num_i2(ifile)=str2double(str_2);
+    if isnan(num_i2(ifile))
+        num_i2(ifile)=num_i1(ifile);
+    end
+    num_j1(ifile)=stra2num(str_a);
+    if isnan(num_j1(ifile))
+        num_j1(ifile)=1;
+    end
+    num_j2(ifile)=stra2num(str_b);
+    if isnan(num_j2(ifile))
+        num_j2(ifile)=num_j1(ifile);
+    end
+end
+

trunk/src/series/merge_proj.m

@@ -1 @@
-function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series);
+function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series)
 
 %requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
@@ -65 +65 @@
     if ~isequal(hhh,'')&& mmreader.isPlatformSupported()
         if isequal(lower(FileExt{iview}),'.avi')
-            MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}]));
+            MovieObject{iview}=mmreader(fullfile(Series.RootPath{iview},[Series.RootFile{iview} Series.FileExt{iview}]));
             test_movie(iview)=1;
         end
@@ -117 +117 @@
 %check coincidence in time
 multitime=0;
-if length(timecell)==0
+if isempty(timecell)
     time=[];
 elseif length(timecell)==1
@@ -160 +160 @@
 if isequal(FieldName,'get_field...')
     hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI
-   % hhget_field=guidata(hget_field);%handles of GUI elements in get_field
     SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI
-%     if isequal(get(hhget_field.menu_coord,'Visible'),'on')
-%         list_transform=get(hhget_field.menu_coord,'String');
-%         val_list=get(hhget_field.menu_coord,'Value');
-%         transform=list_transform{val_list};
-%     end
 end
 %detect whether all the files are 'images' or 'netcdf'
@@ -176 +170 @@
 for iview=1:nbview
      ext=FileExt{iview};
-     form=imformats(ext([2:end]));
+     form=imformats(ext(2:end));
      if isequal(lower(ext),'.vol')
          testvol=testvol+1;
@@ -286 +280 @@
                 Field{iview}=transform_fct(Field{iview},XmlData{iview});%transform to phys if requested
             end
+            min(Field{iview}.X)
             if testcivx
                     Field{iview}=calc_field(FieldName,Field{iview});
             end
+            min(Field{iview}.X)
 
             %projection on object (gridded plane)
@@ -386 +382 @@
         error=1;
     end
-%      if ~isequal(MergeData.VarDimIndex,Data{iview}.VarDimIndex)
-%         error=1;
-%      end
 end
 if error
@@ -394 +387 @@
     return
 end
+
+%group the variables (fields of 'FieldData') in cells of variables with the same dimensions
+[CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1});
+%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
+% CellVarIndex=cells of variable index arrays
+ivar_new=0; % index of the current variable in the projected field
+icoord=0;
+for icell=1:length(CellVarIndex)
+    if NbDim(icell)==1
+        continue
+    end
+    VarIndex=CellVarIndex{icell};%  indices of the selected variables in the list FieldData.ListVarName
+    VarType=VarTypeCell{icell};
+    ivar_X=VarType.coord_x;
+    ivar_Y=VarType.coord_y;
+    ivar_FF=VarType.errorflag;
+    if isempty(ivar_X)
+        test_grid=1;%test for input data on regular grid (e.g. image)coordinates
+    else
+        if length(ivar_Y)~=1
+                msgbox_uvmat('ERROR','y coordinate missing in proj_field.m')
+                return
+        end
+        test_grid=0;
+    end
+%    DimIndices=Data{1}.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell)
+    %case of input fields with unstructured coordinates
+    if ~test_grid
+        for ivar=VarIndex
+            VarName=MergeData.ListVarName{ivar};
+            for iview=1:nbview
+                eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName '];'])
+            end
+        end
+    %case of fields defined on a structured  grid 
+    else  
+%        DimValue=MergeData.DimValue(DimIndices);%set of dimension values
+        testFF=0;
+        for iview=2:nbview
+%             if ~isequal(DimValue,Data{iview}.DimValue(DimIndices))
+%                 MergeData.Txt='ERROR: attempt at merging structured fields with different sizes';
+%                 return
+%             end
+            for ivar=VarIndex
+                VarName=MergeData.ListVarName{ivar};
+                if isfield(MergeData,'VarAttribute')
+                    if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag')
+                        testFF=1;
+                    end
+                end
+                eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';'])
+            end
+        end
+        if testFF
+            nbaver=nbview-MergeData.FF;
+            indgood=find(nbaver>0);
+            for ivar=VarIndex
+                VarName=MergeData.ListVarName{ivar};
+                eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);'])
+            end 
+        else
+            for ivar=VarIndex
+                VarName=MergeData.ListVarName{ivar};
+                eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;'])
+            end    
+        end
+    end
+end
+    

trunk/src/series/sub_background.m

@@ -65 +65 @@
 FileType=[];%default
 MovieObject=[];
+FileExt=Series.FileExt;
+
 if isequal(lower(FileExt),'.avi')
     hhh=which('mmreader');
@@ -78 +80 @@
    form=imformats(FileExt(2:end));
    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
-       if isequal(NomType,'*');
+       if isequal(Series.NomType,'*');
            FileType='multimage';
        else
@@ -237 +239 @@
         ifile=indselect(ifield);
         filename=name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt,Series.NomType);
-        Aread=read_image(filename,FileType,num_i1(ifile),movieobject);
+        Aread=read_image(filename,FileType,num_i1(ifile),MovieObject);
         Ak(:,:,ifield)=Aread;           
     end
@@ -272 +274 @@
                     ifile=indselect(ifield+step*floor(nbaver/2)+iburst-1);
                     filename=name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt,Series.NomType);
-                    Aread=read_image(filename,FileType,num_i1(ifile),movieobject);
+                    Aread=read_image(filename,FileType,num_i1(ifile),MovieObject);
                     Ak(:,:,nbaver_ima-step+iburst)=Aread;
                 end
@@ -316 +318 @@
 %------------------------------------------------------------------------
 %--read images and convert them to the uint16 format used for PIV
-function A=read_image(filename,type_ima,num,movieobject)
+function A=read_image(filename,type_ima,num,MovieObject)
 %------------------------------------------------------------------------
 %num is the view number needed for an avi movie
 switch type_ima
     case 'movie'
-        A=read(movieobject,num);
+        A=read(MovieObject,num);
     case 'avi'
         mov=aviread(filename,num);

trunk/src/stra2num.m

@@ -12 +12 @@
 
 function numres=stra2num(str)
-numres=[]; %default
+numres=NaN; %default
 if double(str) >= 48 & double(str) <= 57 % = test for number strings
-    numres=str2num(str);
+    numres=str2double(str);
 elseif double(str) >= 65 & double(str) <= 90 % test on ascii code for capital letters
     numres=double(str)-64; %change capital letters to corresponding number in the alphabet

trunk/src/sub_field.m

@@ -202 +202 @@
                 V_1 =interp2(X_1,Y_1,V_1,x,y');
            end
-           val(['SubData.' UName '=Field.' UName '-U_1;'])
-           val(['SubData.' VName '=Field.' VName '-V_1;'])
+           eval(['SubData.' UName '=Field.' UName '-U_1;'])
+           eval(['SubData.' VName '=Field.' VName '-V_1;'])
        else
            AName=Field.ListVarName{ivar_C};

trunk/src/uvmat.m

@@ -165 +165 @@
 % Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
 % nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
-%-------------------------------------------------------------------
-%-------------------------------------------------------------------
+
+%------------------------------------------------------------------------
+%------------------------------------------------------------------------
 %  I - MAIN FUNCTION UVMAT (DO NOT MODIFY)
-%-------------------------------------------------------------------
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
+%------------------------------------------------------------------------
 function varargout = uvmat(varargin)
 
@@ -191 +192 @@
 % End initialization code - DO NOT EDIT
 
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes just before uvmat is made visible.
 function uvmat_OpeningFcn(hObject, eventdata, handles, input )
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
 global nb_builtin
 
@@ -221 +222 @@
 set(hObject,'DeleteFcn',{@closefcn})%
 
-%TRANSFORM menu: loads the information stored in prefdir to initiate the browser and the list of functions
+%refresh projection plane
+UvData.Object{1}.Style='plane';%main plotting plane
+UvData.Object{1}.ProjMode='projection';%main plotting plane
+if ~isfield(UvData.Object{1},'plotaxes')
+    UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
+    set(handles.list_object_1,'Value',1);
+    set(handles.list_object_1,'String',{'1-PLANE'});
+end
+
+%TRANSFORM menu: builtin fcts
 menu_str={'';'phys';'px';'phys_polar'};
 nb_builtin=numel(menu_str); %number of functions
@@ -238 +248 @@
 end
 rmpath(fullfile(path_uvmat,'transform_field'))
-
-%refresh projection plane
-UvData.Object{1}.Style='plane';%main plotting plane
-UvData.Object{1}.ProjMode='projection';%main plotting plane
-if ~isfield(UvData.Object{1},'plotaxes')
-    UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
-    set(handles.list_object_1,'Value',1);
-    set(handles.list_object_1,'String',{'1-PLANE'});
-end
 
 %load the list of previously browsed files in menus Open and Open_1
@@ -279 +280 @@
              if exist(file,'file')
                 h_func=str2func(file);
-                testexist=[testexist 1]; %#ok<AGROW>
+                testexist=[testexist 1]; 
              else
                 h_func=[];
-                testexist=[testexist 0];  %#ok<AGROW>
+                testexist=[testexist 0]; 
              end
-             fct_handle=[fct_handle; {h_func}];%#ok<AGROW> %concatene the list of paths
+             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
              rmpath(path)
-             menu_str=[menu_str; {file}]; %#ok<AGROW>
+             menu_str=[menu_str; {file}]; 
          end
       end
@@ -344 +345 @@
         set(handles.Fields,'Value',1)
         set(handles.Fields,'String',{'get_field...'})    
-       % set(handles.Fields,'UserData',Field)
         testinputfield=1;
         
@@ -577 +577 @@
             [ff,rr,FileBase_1,ii,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
             NomType_1=get(handles.FileIndex_1,'UserData');     
-            FileName_1=name_generator(FileBase_1,stra2num(i1),stra2num(i2),FileExt_1,NomType_1,1,stra2num(str_a),stra2num(str_b),SubDir_1);
+            FileName_1=name_generator(FileBase_1,str2double(i1),str2double(i2),FileExt_1,NomType_1,1,stra2num(str_a),stra2num(str_b),SubDir_1);
             if exist(FileName_1,'file')
-                FileIndex_1=name_generator('',stra2num(i1),stra2num(i2),'',NomType_1,1,stra2num(str_a),stra2num(str_b),'');
+                FileIndex_1=name_generator('',str2double(i1),str2double(i2),'',NomType_1,1,stra2num(str_a),stra2num(str_b),'');
                 set(handles.FileIndex_1,'String',FileIndex_1)
             else
@@ -608 +608 @@
 end
 
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
 function RootPath_Callback(hObject,eventdata,handles)
+%------------------------------------------------------------------------
 update_rootinfo(hObject,eventdata,handles);
 
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
 %-- called by action in RootFile edit box
-%-------------------------------------------------------------------
 function SubDir_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 %refresh the menu of input fields
 Fields_Callback(hObject, eventdata, handles);
@@ -621 +622 @@
 run0_Callback(hObject, eventdata, handles); 
 
-
-%-------------------------------------------------------------------
-%-- called by action in RootFile edit box
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
+% --- called by action in RootFile edit box
 function RootFile_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 update_rootinfo(hObject,eventdata,handles)
 
-%-------------------------------------------------------------------
-%-- called by action in FileIndex edit box
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
+% --- called by action in FileIndex edit box
 function FileIndex_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 FileIndices=get(handles.FileIndex,'String');
 if isempty(str2num(FileIndices))
@@ -647 +647 @@
 run0_Callback(hObject, eventdata, handles)
 
-%-------------------------------------------------------------------
-%-- called by action in FileIndex_1 edit box
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
+% --- called by action in FileIndex_1 edit box
 function FileIndex_1_Callback(hObject, eventdata, handles)
-% FileIndices=get(handles.FileIndex_1,'String');
-% if isempty(str2num(FileIndices))
-%     [pp,ff,str1,str2,str_a,str_b]=name2display(FileIndices)
-% else
-%     str1=FileIndices;
-%     str2='';
-%     str_a='';
-%     str_b='';
-% end
-% set(handles.i1,'String',str1);
-% set(handles.i2,'String',str2);
-% set(handles.j1,'String',str_a);
-% set(handles.j2,'String',str_b);
+%------------------------------------------------------------------------
 run0_Callback(hObject, eventdata, handles)
 
-%-------------------------------------------------------------------
-% -- update information about a new field series (indices to scan, timing, calibration from an xml file, then refresh current plots
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
+% --- update information about a new field series (indices to scan, timing, calibration from an xml file, then refresh current plots
 function update_rootinfo(hObject,eventdata,handles)
-
+%------------------------------------------------------------------------
 set(handles.RootPath,'BackgroundColor',[1 1 0])
 drawnow
@@ -678 +664 @@
 UvData.TestInputFile=1;
 set(handles.fix_pair,'Value',1) % activate by default the comp_input '-'input window
-%FileIndex_Callback(hObject, eventdata, handles)% update field counters
 
 [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
@@ -693 +678 @@
 TimeUnit=[];%default
 testima=0; %test for image input
+imainfo=[];
+ColorType='falsecolor'; %default
+hhh='';
 if isequal(lower(FileExt),'.avi') %.avi file
     testima=1;
-    info=aviinfo([FileBase FileIndices FileExt]);
-    nbfield=info.NumFrames;
+    imainfo=aviinfo([FileBase FileIndices FileExt]);
+    nbfield=imainfo.NumFrames;
     nburst=1;
-    set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
-    XmlData.Time=(0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond)';
+    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
+    XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
     TimeUnit='s';
-    set(handles.npx,'String',num2str(info.Width));%fills nbre of pixels x box
-    set(handles.npy,'String',num2str(info.Height));%fills nbre of pixels y box
     hhh=which('mmreader');
-    if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
-        UvData.MovieObject=mmreader([FileBase FileIndices FileExt]);
-    end
+    ColorType=imainfo.ImageType;%='truecolor' for color images
 elseif ~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol')%&& isequal(NomType,'*')% multi-frame image
     testima=1;
@@ -715 +699 @@
         imainfo=imfinfo([FileBase FileIndices FileExt]);
     end
+    ColorType=imainfo.ColorType;%='truecolor' for color images
     if length(imainfo) >1 %case of image with multiple frames
         nbfield=length(imainfo);
         nburst=1;
     end 
-    if isfield(UvData,'MovieObject')
-        UvData=rmfield(UvData,'MovieObject');
-    end
-else 
-    %set(handles.last_i,'String','');%fills last_field box
+end
+if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
+    UvData.MovieObject=mmreader([FileBase FileIndices FileExt]);
+elseif isfield(UvData,'MovieObject')
+    UvData=rmfield(UvData,'MovieObject');
+end
+if isfield(imainfo,'Width') && isfield(imainfo,'Height')
+    set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
+    set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
+else
     set(handles.npx,'String','');%fills nbre of pixels x box
-    set(handles.npy,'String','');%fills nbre of pixels y box
-    if isfield(UvData,'MovieObject')
-        UvData=rmfield(UvData,'MovieObject');
-    end
-end
+    set(handles.npy,'String','');%fills nbre of pixels x box
+end
+set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
 
 % read parameters (time, geometric calibration..) from a documentation file (.xml advised)
@@ -821 +809 @@
         set(handles.transform_fct,'Value',1); %  no transform by default
     else
-        if (isfield(GeometryCalib,'R')& ~isequal(GeometryCalib.R(2,1),0) & ~isequal(GeometryCalib.R(1,2),0)) |...
-            (isfield(GeometryCalib,'kappa1')& ~isequal(GeometryCalib.kappa1,0))
+        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) |...
+            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
             set(handles.pxcm,'String','var')
             set(handles.pycm,'String','var')
@@ -835 +823 @@
         end
         if isfield(GeometryCalib,'SliceCoord')
+            
            siz=size(GeometryCalib.SliceCoord);
            if siz(1)>1
@@ -847 +836 @@
            end
            slices_Callback(hObject, eventdata, handles)
-    %        Coord=UvData.XmlData.GeometryCalib.SliceCoord;
-    %        ZIndex=num_i1-NbSlice*(floor((num_i1-1)/NbSlice));
-        end
-
-            
+        end           
     end
 end
 
 %update the data attached to the uvmat interface
-% set(handles.nb_slice,'String',num2str(NbSlice)) 
 if ~isempty(TimeUnit)
     set(handles.time_txt,'String',['time (' TimeUnit ')'])
 end
-%set(handles.DtUnit,'String',['10^(-3)' TimeUnit])
 UvData.TimeUnit=TimeUnit;
 UvData.XmlData=XmlData;
@@ -986 +969 @@
 end
 sizf=size(fileinput_1);
-if (~ischar(fileinput_1)|~isequal(sizf(1),1)),return;end
+if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
 
 % refresh the current displayed field
@@ -1197 +1180 @@
 end
 TimeUnit_1=[];
-% testima=0; %test for image input
+hhh='';%default, test for  movie reading with mmreader
+imainfo=[];
 if isequal(lower(FileExt),'.avi') %.avi file
-%     testima=1;
-    info=aviinfo([FileBase FileIndices FileExt]);
-    nbfield_1=info.NumFrames;
+    imainfo=aviinfo([FileBase FileIndices FileExt]);
+    nbfield_1=imainfo.NumFrames;
     nburst_1=1;
-    %set(handles.last_i,'String',num2str(info.NumFrames));%fills last_field box
     set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
-%     set(handles.dt,'UserData',info.FramesPerSecond);
-    time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]';
-    npx=get(handles.npx,'String');
-    npy=get(handles.npy,'String');
-    if isequal(npx,'') || isequal(npy,'')
-        set(handles.npx,'String',num2str(info.Width));%fills nbre of pixels x box
-        set(handles.npy,'String',num2str(info.Height));%fills nbre of pixels y box
-    end
-elseif ~isempty(imformats(FileExt(2:end))) %&& isequal(NomType,'*')% multi-frame image
+    time=[0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond]';
+    ColorType=imainfo.ImageType;%='truecolor' for color images
+    hhh=which('mmreader');
+elseif ~isempty(imformats(FileExt(2:end)))|| isequal(FileExt,'.vol')
     testima=1;
-    imainfo=imfinfo([FileBase FileIndices FileExt]);  
+    if ~isequal(SubDir,'')
+        RootFile=get(handles.RootFile,'String');
+        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
+    else
+        imainfo=imfinfo([FileBase FileIndices FileExt]);
+    end
+    ColorType=imainfo.ColorType;%='truecolor' for color images
     if length(imainfo) >1 %case of image with multiple frames
         nbfield_1=length(imainfo);
         nburst_1=1;
-        %set(handles.last_i,'String',num2str(length(imainfo)));%fills last_field box
-    end       
-else 
-    %set(handles.last_i,'String','');%fills last_field box
-    set(handles.npx,'String','');%fills nbre of pixels x box
-    set(handles.npy,'String','');%fills nbre of pixels y box 
+    end 
+end
+if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
+    UvData.MovieObject_1=mmreader([FileBase FileIndices FileExt]);
+elseif isfield(UvData,'MovieObject_1')
+    UvData=rmfield(UvData,'MovieObject_1');
+end
+if strcmp(get(handles.npx,'String'),'') || strcmp(get(handles.npy,'String'),'')%update npx and npy if it is not already filled by the first input field
+    if  isfield(imainfo,'Width') && isfield(imainfo,'Height')
+        set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
+        set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
+    else
+        set(handles.npx,'String','');%fills nbre of pixels x box
+        set(handles.npy,'String','');%fills nbre of pixels x box
+    end
+    set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
 end
 
@@ -1849 +1842 @@
 end
 
-num_i1=stra2num(get(handles.i1,'String'));
+num_i1=str2double(get(handles.i1,'String'));
 num_j1=stra2num(get(handles.j1,'String'));
-num_i2=stra2num(get(handles.i2,'String'));
+num_i2=str2double(get(handles.i2,'String'));
 num_j2=stra2num(get(handles.j2,'String'));
-if isempty(num_j2)
+if isnan(num_j2)
     if isempty(num_i2)   
         msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
@@ -1862 +1855 @@
     end
 end
-if isempty(num_i2)
+if isnan(num_i2)
     num_i2=num_i1;%repeat the index i1 by default
 end
@@ -2238 +2231 @@
     if isequal(FileType,'netcdf')  %read the first nc field
         if isequal(FieldName,'get_field...')% read the field names on the interface get_field.
-            %VelType=get(handles.Fields,'UserData');
-            hget_field=findobj(allchild(0),'Name','get_field')%find the get_field... GUI
+            hget_field=findobj(allchild(0),'Name','uvmat_field');%find the get_field... GUI
             if isempty(hget_field)
-                hget_field= get_field(filename);%open the get_field GUI    
-            end
-            if numel(hget_field)>1%case of several get_field GUI
-                hget_field=hget_field(1);
+                hget_field= get_field(filename);%open the get_field GUI   
+                set(hget_field,'name','uvmat_field')
+            elseif UvData.NewSeries
+                delete(hget_field)
+                hget_field= get_field(filename);%open the get_field GUI 
+                set(hget_field,'name','uvmat_field')
             end
             hhget_field=guidata(hget_field);
-            set(hhget_field.inputfile,'String',filename)% update the list of input fields in get_field
-            set(hhget_field.ACTION,'Value',1)% PLOT option selected
-            set(hhget_field.list_fig,'Value',2)% plotting axes =uvmat selected
-            [Field{1},errormsg]=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
-            if ~isempty(errormsg)
-                errormsg=['error in uvmat/run0_Callback/read_get_field: ' errormsg];
-                return
-            end
+            funct_list=get(hhget_field.ACTION,'UserData');
+            funct_index=get(hhget_field.ACTION,'Value');
+            funct=funct_list{funct_index};
+            Field{1}=funct(hget_field); %read the names of the variables to plot in the get_field GUI
             CivStage=0;
-            VelType_out=[];         
+            VelType_out=[];    
         else
             [Field{1},VelType_out]=read_civxdata(filename,InputField,VelType);
@@ -2269 +2259 @@
     if ~isempty(filename_1) && ~test_keepdata_1 && isequal(FileType_1,'netcdf') %read the second file
         if isequal(FieldName_1,'get_field...')% read the field names on the interface get_field.
-            hget_field=findobj(allchild(0),'Name','get_field_1');%find the get_field... GUI
-             if isempty(hget_field)
-                 hget_field= get_field(filename_1);%open the get_field GUI
-                 set(hget_field,'name','get_field_1')
-%                 enable_transform(handles,'off')% no field transform (possible transform in the GUI get_field)
-             end
-            hhget_field=guidata(hget_field);%handles of GUI elements in get_field
-            SubField=get_field('read_var_names',hObject,eventdata,hhget_field); %read the names of the variables to plot in the get_field GUI 
-            [Field{2},var_detect]=nc2struct(filename_1,SubField.ListVarName); %read the corresponding input data                
-            Field{2}.VarAttribute=SubField.VarAttribute;
-            %update the display on get_field
-            set(hhget_field.inputfile,'String',filename_1)
-            set(hhget_field.variables,'Value',1)
-            Tabchar={''};%default
-            Tabcell=[];
-            if isfield(Field{2},'ListGlobalAttribute')& ~isempty(Field{2}.ListGlobalAttribute)
-                for iline=1:length(Field{2}.ListGlobalAttribute)
-                    Tabcell{iline,1}=Field{2}.ListGlobalAttribute{iline};
-                    if isfield(Field{2}, Field{2}.ListGlobalAttribute{iline})
-                        eval(['val=Field{2}.' Field{2}.ListGlobalAttribute{iline} ';'])
-                        if ischar(val);
-                            Tabcell{iline,2}=val;
-                        else
-                            Tabcell{iline,2}=num2str(val);
-                        end
-                    end
-                end
-                if ~isempty(Tabcell)
-                    Tabchar=cell2tab(Tabcell,'=');
-                    Tabchar=[{''};Tabchar];
-                end
+            hget_field_1=findobj(allchild(0),'Name','uvmat_field_1');%find the get_field... GUI
+            if isempty(hget_field_1)
+                 hget_field_1= get_field(filename_1);%open the get_field GUI
+                 set(hget_field_1,'name','uvmat_field_1')
             end
-            set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field 
+            hhget_field_1=guidata(hget_field_1);%handles of GUI elements in get_field
+            funct_list=get(hhget_field_1.ACTION,'UserData');
+            funct_index=get(hhget_field_1.ACTION,'Value');
+            funct=funct_list{funct_index};
+            Field{2}=funct(hget_field_1); %read the names of the variables to plot in the get_field GUI
         else
             [Field{2},VelType_out_1]=read_civxdata(filename_1,InputField_1,VelType_1);
@@ -2379 +2346 @@
        if siz(1)>1
            NbSlice=siz(1);
-%            set(handles.slices,'Visible','on')
-%            set(handles.slices,'Value',1)
        else
            NbSlice=1;
        end
-       %set(handles.nb_slice,'String',num2str(NbSlice))
-%        slices_Callback(handles.uvmat, [], handles)
 end
 
@@ -2510 +2473 @@
 end
 %case of structured coordinates
-if isfield(UvData.Field,'AX') & isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')
+if isfield(UvData.Field,'AX') && isfield(UvData.Field,'AY')&& isfield(UvData.Field,'A')
     UvData.XMax=max(UvData.Field.AX);
     UvData.XMin=min(UvData.Field.AX);
@@ -2518 +2481 @@
     UvData.Mesh=sqrt((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)/((np_A(1)-1) * (np_A(2)-1))) ; 
 end
-if  isempty(coord_x)&~isempty(CellVarIndex)
+if  isempty(coord_x) && ~isempty(CellVarIndex)
     VarIndex=CellVarIndex{imax}; % list of variable indices
     DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
@@ -2640 +2603 @@
         %Projeter les champs sur l'objet:*
         ObjectData=proj_field(UvData.Field,UvData.Object{iobj},iobj);
-%         if imap==2
-%             UvData.ProjField_2=ObjectData;%store the projection field on uvmat: ***** WILL REPLACE THE FIELD SORED ON THE AXES: AxeData *****
-%         else
-%             UvData.ProjField_1=ObjectData;%store the projection field on view_field
-%         end
         %use of mask
         if isfield(ObjectData,'NbDim')&isequal(ObjectData.NbDim,2)
@@ -2778 +2736 @@
 testimedoc=0;
 if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'Time')
-    if isempty(num_i2)
+    if isempty(num_i2)||isnan(num_i2)
         num_i2=num_i1;
     end
-    if isempty(num_j1)
+    if isempty(num_j1)||isnan(num_j1)
         num_j1=1;
     end
-    if isempty(num_j2)
+    if isempty(num_j2)||isnan(num_j2)
         num_j2=num_j1;
     end
@@ -2828 +2786 @@
     end
 end
-
+%update the input file name in the get_field GUI
+if isequal(FieldName,'get_field...')
+    set(hhget_field.inputfile,'String',filename)
+    Tabchar={''};%default
+    Tabcell=[];
+    if isfield(Field{1},'ListGlobalAttribute')& ~isempty(Field{1}.ListGlobalAttribute)
+        for iline=1:length(Field{1}.ListGlobalAttribute)
+            Tabcell{iline,1}=Field{1}.ListGlobalAttribute{iline};
+            if isfield(Field{1}, Field{1}.ListGlobalAttribute{iline})
+                eval(['val=Field{1}.' Field{1}.ListGlobalAttribute{iline} ';'])
+                if ischar(val);
+                    Tabcell{iline,2}=val;
+                else
+                    Tabcell{iline,2}=num2str(val);
+                end
+            end
+        end
+        if ~isempty(Tabcell)
+            Tabchar=cell2tab(Tabcell,'=');
+            Tabchar=[{''};Tabchar];
+        end
+    end
+    set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field 
+end
+if isequal(FieldName_1,'get_field...')
+    set(hhget_field_1.inputfile,'String',filename_1)
+    Tabchar={''};%default
+    Tabcell=[];
+    if isfield(Field{2},'ListGlobalAttribute')& ~isempty(Field{2}.ListGlobalAttribute)
+        for iline=1:length(Field{2}.ListGlobalAttribute)
+            Tabcell{iline,1}=Field{2}.ListGlobalAttribute{iline};
+            if isfield(Field{2}, Field{2}.ListGlobalAttribute{iline})
+                eval(['val=Field{2}.' Field{2}.ListGlobalAttribute{iline} ';'])
+                if ischar(val);
+                    Tabcell{iline,2}=val;
+                else
+                    Tabcell{iline,2}=num2str(val);
+                end
+            end
+        end
+        if ~isempty(Tabcell)
+            Tabchar=cell2tab(Tabcell,'=');
+            Tabchar=[{''};Tabchar];
+        end
+    end
+    set(hhget_field_1.attributes,'String',Tabchar);%update list of global attributes in get_field 
+end
 
 
@@ -2858 +2862 @@
     set(handles.auto_xy,'BackgroundColor',[1 1 0])
     cla(handles.axes3)
-    update_plot(handles)
+    update_plot(handles);
 else
     set(handles.auto_xy,'BackgroundColor',[0.7 0.7 0.7])
-    update_plot(handles)
+    update_plot(handles);
 %     axis(handles.axes3,'image')
 end
@@ -3039 +3043 @@
 end
 
-% %----------------------------------------------
-% %read the data displayed for the input rootfile windows (new)
-% %-------------------------------------------------
+%------------------------------------------------------------------------
+% --- read the data displayed for the input rootfile windows (new)
 function [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles)
+%------------------------------------------------------------------------
 RootPath=get(handles.RootPath,'String');
 FileName=RootPath; %default
@@ -3114 +3118 @@
      set_veltype_display(veltype_handles,0) % unvisible civ buttons
      filename=read_file_boxes(handles);
-     hget_field=findobj(allchild(0),'name','get_field');
-     if ~isempty(hget_field)
-         delete(hget_field)
+     hget_field=findobj(allchild(0),'name','uvmat_field');
+     if isempty(hget_field)
+         hget_field=get_field(filename);
+         set(hget_field,'Name','uvmat_field')        
      end
-     get_field(filename)
     return %no action
 end
@@ -3849 +3853 @@
 % set(handles.slider1,'Value',col) 
 set_vec_col_bar(handles)
-update_plot(handles)
+update_plot(handles);
 
 %----------------------------------------------------------------
@@ -3859 +3863 @@
 % slider2_Callback(hObject, eventdata, handles)
 set_vec_col_bar(handles)
-update_plot(handles)
+update_plot(handles);
 %------------------------------------------------------------
 %update the slider values after displaying vectors
@@ -3885 +3889 @@
 set_vec_col_bar(handles)
 
-% %--------------------------------------------
-% %update the display of color code for vectors
-% %--------------------------------------------
-% function set_vec_col_bar(handles)
-% %get the image of the color display button 'vec_col_bar' in pixels
-% uni=get(handles.vec_col_bar,'Unit');
-% set(handles.vec_col_bar,'Unit','pixel')
-% pos_vert=get(handles.vec_col_bar,'Position');
-% set(handles.vec_col_bar,'Unit','Normalized')
-% width=ceil(pos_vert(3));
-% height=ceil(pos_vert(4));
-% %get slider indications
-% colcode.min=get(handles.slider1,'Min');
-% colcode.max=get(handles.slider1,'Max');
-% colcode.colcode1=get(handles.slider1,'Value');
-% colcode.colcode2=get(handles.slider2,'Value');
-% colcode.option=get(handles.vec_col_bar,'Value');
-% colcode.auto=1;
-% list_code=get(handles.col_vec,'String');% list menu fields
-% index_code=get(handles.col_vec,'Value');% selected string index
-% colcode.CName= list_code{index_code(1)}; % selected field used for vector color
-% vec_C=colcode.min+(colcode.max-colcode.min)*[0.5:width-0.5]/width;%sample of vec_C values from min to max
-% [colorlist,col_vec]=set_col_vec(colcode,vec_C);
-% oneheight=ones(1,height);
-% A1=colorlist(col_vec,1)*oneheight;
-% A2=colorlist(col_vec,2)*oneheight;
-% A3=colorlist(col_vec,3)*oneheight;
-% A(:,:,1)=A1';
-% A(:,:,2)=A2';
-% A(:,:,3)=A3';
-% set(handles.vec_col_bar,'Cdata',A)
-
-%--------------------------------------------------------
-% --- Executes on button press in cal.
-function cal_Callback(hObject, eventdata, handles)
-
-
-
 %-------------------------------------------------------------
 % --- Executes on selection change in transform_fct.
@@ -3940 +3906 @@
     dlg_title = 'user defined transform';
     num_lines= 1;
-    [FileName, PathName, filterindex] = uigetfile( ...
+    [FileName, PathName] = uigetfile( ...
        {'*.m', ' (*.m)';
         '*.m',  '.m files '; ...
@@ -4015 +3981 @@
 list_object_2_Callback(hObject, eventdata, handles)
 
-
-
 %delete mask if it is displayed 
 if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
@@ -4115 +4079 @@
 set(handles.AutoScal,'Value',1) %suppress auto mode
 set(handles.AutoScal,'BackgroundColor',[1 1 0])
-update_plot(handles)
+update_plot(handles);
 
 %-----------------------------------------------------------------
@@ -4122 +4086 @@
 set(handles.AutoScal,'Value',1) %suppress auto mode
 set(handles.AutoScal,'BackgroundColor',[1 1 0])
-update_plot(handles)
+update_plot(handles);
 
 %-----------------------------------------------
@@ -4133 +4097 @@
     set(handles.AutoScal,'BackgroundColor',[0.7 0.7 0.7])
     update_plot(handles);
-%     set(handles.MinA,'String',num2str(ScalOut.MinA,3))
-%     set(handles.MaxA,'String',num2str(ScalOut.MaxA,3))
 end
 
@@ -4140 +4102 @@
 function BW_Callback(hObject, eventdata, handles)
 %-------------------------------------------------------------------
-update_plot(handles)
+update_plot(handles);
 
 %-------------------------------------------------------------------
@@ -4153 +4115 @@
     set(handles.IncrA,'Visible','off')
 end
-update_plot(handles)
+update_plot(handles);
 
 %-------------------------------------------------------------------
 function IncrA_Callback(hObject, eventdata, handles)
 %-------------------------------------------------------------------
-update_plot(handles)
+update_plot(handles);
 
 %-------------------------------------------------------------------
 function HideWarning_Callback(hObject, eventdata, handles)
 %-------------------------------------------------------------------
-update_plot(handles)
+update_plot(handles);
 
 %-------------------------------------------------------------------
 function HideFalse_Callback(hObject, eventdata, handles)
 %-------------------------------------------------------------------
-update_plot(handles)
+update_plot(handles);
 
 %-------------------------------------------------------------------
@@ -4175 +4137 @@
 set(handles.AutoVec,'Value',1);
 set(handles.AutoVec,'BackgroundColor',[1 1 0])
-update_plot(handles)
+update_plot(handles);
 
 %-------------------------------------------------------------------
@@ -4189 +4151 @@
 end
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on selection change in decimate4 (nb_vec/4).
-%-------------------------------------------------------
 function decimate4_Callback(hObject, eventdata, handles)
-update_plot(handles)
-
-
-%-------------------------------------------------------
+%------------------------------------------------------------------------
+update_plot(handles);
+
+%------------------------------------------------------------------------
 % --- Executes on selection change in color_code menu
-%-------------------------------------------------------
 function color_code_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 set_vec_col_bar(handles)
 update_plot(handles);
 
-%-------------------------------------------------------
+%------------------------------------------------------------------------
 % --- Executes on button press in AutoVecColor.
-%-------------------------------------------------------
 function AutoVecColor_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 test=get(handles.AutoVecColor,'Value');
 if test
@@ -4215 +4176 @@
     set(handles.AutoVecColor,'BackgroundColor',[0.7 0.7 0.7])
 end
-%set_vec_col_bar(handles)
-
-%-------------------------------------------------------
+
+%------------------------------------------------------------------------
 % --- Executes on selection change in max_vec.
-%-------------------------------------------------------
 function min_vec_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 max_vec_Callback(hObject, eventdata, handles)
 
+%------------------------------------------------------------------------
 % --- Executes on selection change in max_vec.
 function max_vec_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 set(handles.AutoVecColor,'Value',1)
 AutoVecColor_Callback(hObject, eventdata, handles)
@@ -4237 +4199 @@
 update_plot(handles);
 
-%-------------------------------------------------------------------
-%update the display of color code for vectors
+%------------------------------------------------------------------------
+% --- update the display of color code for vectors
 function set_vec_col_bar(handles)
-%-------------------------------------------------------------------
+%------------------------------------------------------------------------
 %get the image of the color display button 'vec_col_bar' in pixels
 set(handles.vec_col_bar,'Unit','pixel');
@@ -4283 +4245 @@
 AxeData=get(haxes,'UserData');
 PlotParam=read_plot_param(handles);
+PlotParam.Scalar
 [PlotType,PlotParamOut]= plot_field(AxeData,haxes,PlotParam,1);
 write_plot_param(handles,PlotParamOut); %update the auto plot parameters
@@ -4446 +4409 @@
 %------------------------------------------------------
 function MenuExportField_Callback(hObject, eventdata, handles)
-global CurData
-CurData=get(handles.uvmat,'UserData');
-evalin('base','global CurData')%make CurData global in the workspace
+global Data_uvmat
+Data_uvmat=get(handles.uvmat,'UserData');
+evalin('base','global Data_uvmat')%make CurData global in the workspace
 display(['current field :'])
-evalin('base','CurData') %display CurData in the workspace
+evalin('base','Data_uvmat') %display CurData in the workspace
 commandwindow; %brings the Matlab command window to the front
 
@@ -4976 +4939 @@
        '*.xml',  '.xml files '; ...
         '*.mat',  '.mat matlab files '}, ...
-        'Pick a file',get(handles.RootPath,'String'));
+        'Pick an xml Object file',get(handles.RootPath,'String'));
 fileinput=[PathName FileName];%complete file name 
 testblank=findstr(fileinput,' ');%look for blanks