Index: /trunk/src/series/vel2vol.m
===================================================================
--- /trunk/src/series/vel2vol.m	(revision 208)
+++ /trunk/src/series/vel2vol.m	(revision 208)
@@ -0,0 +1,121 @@
+% vel2vol:interpolate 2D velocity fields to volumes with structured coordinates in phys space 
+% (specific to RDvision system)
+%----------------------------------------------------------------------
+function GUI_input=vel2vol(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)
+if ~exist('num_i1','var')
+        GUI_input={'RootPath';'one';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
+        'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
+        'RootFile';'on';... %root input file name ('on' by default)
+        'FileExt';'on';... %input file extension ('on' by default)
+        'NomType';'on';...%type of file indexing ('on' by default)
+        'NbSlice';'on'; ...%nbre of slices ('off' by default)
+        'VelTypeMenu';'one';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
+        'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
+        'CoordType'; 'on';...%can use a transform function
+        'GetObject';'on';...%can use projection object(option 'off'/'one'/'two',
+               ''}
+    return %exit the function 
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%enable waitbar
+hseries=guidata(Series.hseries);%handles of the GUI series
+WaitbarPos=get(hseries.waitbar_frame,'Position');
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% PARAMETERS
+listfield=get(hseries.FieldMenu,'String');
+testfield=get(hseries.FieldMenu,'Value');
+FieldName=listfield{testfield}
+listfield=get(hseries.VelTypeMenu,'String');
+testfield=get(hseries.VelTypeMenu,'Value');
+VelType=listfield{testfield}
+transform_fct=Series.transform_fct;%handles of phys transform function
+
+
+%% projection object (volume)
+test_object=get(hseries.GetObject,'Value');
+if test_object%isfield(Series,'sethandles')
+    hset_object=findobj(allchild(0),'tag','set_object');
+    ProjObject=read_set_object(guidata(hset_object));
+    if ~strcmp(ProjObject.Style,'volume')&&~strcmp(ProjObject.ProjMode,'interp')
+        msgbox_uvmat('ERROR',['a volume with projection mode interp must be defined']);
+        return
+    end
+    answer=msgbox_uvmat('CONFIRMATION',['fields will be interpolated at the grid points of the volume']);
+else
+     answer=msgbox_uvmat('CONFIRMATION',['fields will be concatenated without interpolation']);
+end
+
+%% create dir of the volume velocity fields
+basename=fullfile(Series.RootPath,Series.RootFile) ;
+% [dir_ima,namebase]=fileparts(basename);
+% [path,subdir_ima]=fileparts(dir_ima);
+SubDirNew=[Series.SubDir '_vol'];
+newdir=fullfile(Series.RootPath,SubDirNew);
+mkdir(newdir);
+[xx,msg2] = fileattrib(newdir,'+w','g'); %yield writing access (+w) to user group (g)
+if ~strcmp(msg2,'')
+    msgbox_uvmat('ERROR',['pb of permission for ' subdir_vel ': ' msg2])%error message for directory creation
+    return
+end
+display(['volume fields in the directory ' newdir])
+% basename_new=fullfile(newdir,Series.RootFile);
+
+
+%% read imadoc
+[XmlData,warntext]=imadoc2struct([basename '.xml']);
+nbfield1=size(num_i1,1);
+nbfield2=size(XmlData.Time,2);% use the whole set of j indices
+% set(hseries.first_i,'String',num2str(first_label))% display the first image in the process
+set(hseries.last_j,'String',num2str(nbfield2))% display the last image in the process
+
+%% main loop
+for ifile=1:nbfield1
+    update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield1)
+    for jfile=1:nbfield2
+        filename=name_generator(basename,num_i1(ifile,jfile),num_j1(ifile,jfile),Series.FileExt,Series.NomType,1,num_i2(ifile,jfile),num_j2(ifile,jfile),Series.SubDir);
+        [Field,VelTypeOut]=read_civxdata(filename,FieldName,VelType);
+        if isfield(Field,'Txt')
+            msgbox_uvmat('ERROR',Field.Txt)
+            return
+        end
+        Field.ZIndex=jfile;
+        % coordinate transform
+        Field=transform_fct(Field,XmlData);
+        % concatene slices
+        if jfile==1
+            %             if isempty(Field.absolut_time_T0) || isequal(Field.civ,0)
+            %                 msgbox_uvmat('ERROR','the input file is not civx data')
+            %                 return
+            %             end
+            FieldVol=Field;
+            FieldVol.NbDim=3;
+        else
+            FieldVol.X=[FieldVol.X; Field.X];
+            FieldVol.Y=[FieldVol.Y; Field.Y];
+            FieldVol.Z=[FieldVol.Z; Field.Z];
+            FieldVol.U=[FieldVol.U; Field.U];
+            FieldVol.V=[FieldVol.V; Field.V];
+            if isfield( Field,'F')
+                FieldVol.F=[FieldVol.F; Field.F];
+            end
+        end
+    end
+    if test_object
+        [FieldVol,errormsg]=proj_field(FieldVol,ProjObject);
+        if ~isempty(errormsg)
+            msgbox_uvmat('ERROR',['error in vel2vol/proj_field:' errormsg])
+            return
+        end
+    end
+    filename_new=name_generator(basename,num_i1(ifile,jfile),[],'.nc','_1',1,num_i2(ifile,jfile),[],SubDirNew);
+    errormsg=struct2nc(filename_new,FieldVol);
+    if isempty(errormsg)
+        display([filename_new ' written'])
+    else
+        msgbox_uvmat('ERROR',['error in vel2vol/struct2nc:' errormsg])
+        return
+    end
+end
+