Changeset 867

Timestamp:

Feb 12, 2015, 9:31:47 PM (10 years ago)

Author:

sommeria

Message:

python option added in series and bug corrections

Location:

trunk/src

Files:

• calc_field_tps.m (modified) (2 diffs)
• find_field_bounds.m (modified) (1 diff)
• find_file_series.m (modified) (2 diffs)
• proj_field.m (modified) (5 diffs)
• read_field.m (modified) (1 diff)
• series.m (modified) (17 diffs)
• series/aver_stat.m (modified) (7 diffs)
• series/histo_diff.m (added)
• series/merge_proj.m (modified) (5 diffs)
• series/time_series.m (modified) (1 diff)
• uvmat.m (modified) (3 diffs)

trunk/src/calc_field_tps.m

@@ -105 +105 @@
     VarAttribute=[VarAttribute VarAttributeNew];
 end
-Attr_FF.Role='errorflag';
-VarAttribute=[VarAttribute {Attr_FF}];
+%Attr_FF.Role='errorflag';
+%VarAttribute=[VarAttribute {Attr_FF}];
 FieldName(check_remove)=[];
 
@@ -160 +160 @@
     end
 end
-DataOut.FF=nbval==0; %put errorflag to 1 for points outside the interpolation rang
-nbval(nbval==0)=1;% to avoid division by zero for averaging
+%DataOut.FF=nbval==0; %put errorflag to 1 for points outside the interpolation rang
+nbval(nbval==0)=NaN;% to avoid division by zero for averaging
 ListFieldOut=fieldnames(DataOut);
 for ifield=1:numel(ListFieldOut)

trunk/src/find_field_bounds.m

@@ -41 +41 @@
 NbDim=max(NbDimArray);% spatial dimension of the input field
 imax=find(NbDimArray==NbDim);% indices of field cells to consider
-if isfield(Field,'NbDim')
-    NbDim=double(Field.NbDim);% deal with plane fields containing z coordinates
-end
+% if isfield(Field,'NbDim')
+%     NbDim=double(Field.NbDim);% deal with plane fields containing z coordinates
+% end
 FieldOut.NbDim=NbDim;
 if  NbDim<=1; return; end% stop here for 1D fields

trunk/src/find_file_series.m

@@ -68 +68 @@
     i1_series=[];i2_series=[];j1_series=[];j2_series=[];
     i1_input=1;i2_input=[];j1_input=[];j2_input=[];
+    if ~exist(fullfileinput,'file')
+        RootFile='';
+        return
+    end
 end
 if ~exist(FilePath,'dir')
@@ -74 +78 @@
 if checkfileindexing
 NomTypePref='';
-if isempty(NomType)
+if isempty(NomType)||strcmp(NomType,'*')
     if exist(fullfileinput,'file')
         [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension

trunk/src/proj_field.m

@@ -666 +666 @@
     
     %% identify vector components
-    testU=isfield(CellInfo{icell},'VarIndex_vector_x') &&isfield(CellInfo{icell},'VarIndex_vector_y') ;% test for vectors
+    %testU=isfield(CellInfo{icell},'VarIndex_vector_x') &&isfield(CellInfo{icell},'VarIndex_vector_y') ;% test for vectors
     %     if testU
     %         UName=FieldData.ListVarName{CellInfo{icell}.VarIndex_vector_x};
@@ -700 +700 @@
                     return
                 end
-                ProjData.ListVarName=[ProjData.ListVarName {FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}}];
-                ProjData.VarDimName=[ProjData.VarDimName {FieldData.ListVarName{CellInfo{icell}.CoordIndex(end-1)}}];
+                ProjData.ListVarName=[ProjData.ListVarName FieldData.ListVarName(CellInfo{icell}.CoordIndex(end))];
+                ProjData.VarDimName=[ProjData.VarDimName FieldData.ListVarName(CellInfo{icell}.CoordIndex(end))];
                 nbvar=numel(ProjData.ListVarName);
                 ProjData.VarAttribute{nbvar}.long_name='abscissa along line';
@@ -717 +717 @@
                 ProjData.(FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)})=Xproj;
                 for ivar=1:numel(VarIndex)
-                    ProjData.(VarName{ivar})=FieldData.(VarName{ivar})(flagsel);% restrict vrtibles to the projection band
+                    ProjData.(VarName{ivar})=FieldData.(VarName{ivar})(flagsel);% restrict variables to the projection band
                     ProjData.(VarName{ivar})=ProjData.(VarName{ivar})(indsort);% sort by absissa
                     ProjData.ListVarName=[ProjData.ListVarName VarName{ivar}];
-                    ProjData.VarDimName=[ProjData.VarDimName {FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}}];
+                    ProjData.VarDimName=[ProjData.VarDimName FieldData.ListVarName(CellInfo{icell}.CoordIndex(end))];
                     ProjData.VarAttribute{nbvar+ivar}=FieldData.VarAttribute{VarIndex(ivar)};%reproduce var attribute
                     if isfield(ProjData.VarAttribute{nbvar+ivar},'Role')
                         if  strcmp(ProjData.VarAttribute{nbvar+ivar}.Role,'vector_x');
-                            ivar_U=ivar;
+                            ivar_U=nbvar+ivar;
                         elseif strcmp(ProjData.VarAttribute{nbvar+ivar}.Role,'vector_y');
-                            ivar_V=ivar;
+                            ivar_V=nbvar+ivar;
                         end
                     end
@@ -777 +777 @@
                 end
                 [DataOut,VarAttribute,errormsg]=calc_field_tps(Coord,NbCentres,SubRange,FieldVar,CellInfo{icell}.FieldName,cat(3,XI,YI));
+                ProjData.ListVarName=[ProjData.ListVarName {'X'}];
+                ProjData.VarDimName=[ProjData.VarDimName {'X'}];
                 ProjData.X=Xproj;
                 nbvar=numel(ProjData.ListVarName);
@@ -784 +786 @@
                 ProjData.VarAttribute=[ProjData.VarAttribute VarAttribute];
                 for ivar=1:numel(VarAttribute)
-                    ProjData.VarDimName=[ProjData.VarDimName {XName}];
+                    ProjData.VarDimName=[ProjData.VarDimName {'X'}];
                     if isfield(VarAttribute{ivar},'Role')
                         if  strcmp(VarAttribute{ivar}.Role,'vector_x');

trunk/src/read_field.m

@@ -136 +136 @@
                     Role=[Role {'vector_y'}];
                     ProjModeRequest=[ProjModeRequest {ProjModeRequestVar}];
-                    ListInputField=[ListInputField {''}];
-                    %ListOperator=[ListOperator {[r.Operator '_V']}];
+                    ListInputField=[ListInputField InputField(ilist)];
+                    %ListInputField=[ListInputField {''}];
                 else
                     checkV=1;

trunk/src/series.m

@@ -135 +135 @@
 [path_series,name,ext]=fileparts(which('series'));% path to the GUI series
 path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
-ActionExtList={'.m';'.sh'};% default choice of extensions (Matlab fct .m or compiled version .sh
+ActionExtList={'.m';'.sh';'.py (in dev.)'};% default choice of extensions (Matlab fct .m or compiled version .sh
 ActionPathList=cell(NbBuiltinAction,1);%initiate the cell matrix of Action fct paths
 ActionPathList(:)={path_series_fct}; %set the default path to series fcts to all list members
@@ -620 +620 @@
     if ~exist(RootPath,'dir')
         i1_series=[];
-        RootPath=fileparts(RootPath); %will try the upper folder
+        %RootPath=fileparts(RootPath); %will try the upper folder
+        RootFile='';
     else %scan the input folder
         [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
@@ -626 +627 @@
     end
     % if no file is found, open a browser
-    if isempty(i1_series)
+    if isempty(RootFile)&& isempty(i1_series)
         fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
         if isempty(fileinput)
@@ -722 +723 @@
 if strcmp(iview,'append') % display the input data as a new line in the table
     iview=size(InputTable,1)+1;% the next line in InputTable becomes the current line
-    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
+%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
 elseif strcmp(iview,'one') % refresh the list of  input  file series
     iview=1; %the first line in InputTable becomes the current line
     InputTable={'','','','',''};
-    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
+%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
     set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
     set(handles.MinIndex_i,'Data',[])
@@ -742 +743 @@
     SeriesData.Time={};
 end
+   SeriesData.i1_series(iview+1:end)=[];
+    SeriesData.i2_series(iview+1:end)=[];
+    SeriesData.j1_series(iview+1:end)=[];
+    SeriesData.j2_series(iview+1:end)=[];
+    SeriesData.FileType(iview+1:end)=[];
+    SeriesData.FileInfo(iview+1:end)=[];
+    SeriesData.Time(iview+1:end)=[];
+ InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
 if iview >1
     set(handles.InputLine,'String',num2str(iview))
@@ -1396 +1405 @@
 ActionExt='.m';%default
 if isfield(Param.Action,'ActionExt')
-    ActionExt=Param.Action.ActionExt;% '.m' or '.sh' (compiled)
+    ActionExt=Param.Action.ActionExt;% '.m', '.sh' (compiled)  or '.py' (Python)
     Param.Action=rmfield(Param.Action,'ActionExt');%remove from the recorded xml file to avoid interference during ImportConfig
 end
@@ -1647 +1656 @@
 set(handles.status,'UserData',StatusData)
 
+
+if strcmp(ActionExt, '.py (in dev.)')
+    fprintf([
+        '\n' ...
+        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
+        'The option .py is used. It is still in development.\n' ...
+        'Do not use it unless you really know what you do!\n' ...
+        'To try it, first install Pyp and the most recent version of FluidDyn.\n' ...
+        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
+    RunMode = 'python';
+    t = struct2xml(Param);
+    t = set(t, 1, 'name', 'Series');
+    filexml = fullfile_uvmat(DirXml, '', Param.InputTable{1,3}, '.xml', OutputNomType,...
+         Param.IndexRange.first_i, Param.IndexRange.last_i, first_j, last_j);
+    save(t, filexml);
+end
+
+
 %% direct processing on the current Matlab session
 if strcmp (RunMode,'local')
@@ -1682 +1709 @@
         end
     end
-else
+elseif ~strcmp(RunMode,'python')
     %% processing on a different session of the same computer (background) or cluster, create executable files
     batch_file_list=cell(NbProcess,1);% initiate the list of executable files
@@ -1837 +1864 @@
         system(oar_command);  
         msgbox_uvmat('CONFIRMATION',[ActionName ' launched in cluster: press STATUS to see results'])
+    case 'python'
+        command = [
+            'LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') | [s for s in p if ''matlab'' not in s] | '':''.join(p)") ' ...
+            'python -m fluiddyn.postproc.uvmat ' filexml];
+        % fprintf(['command:\n' command '\n\n'])
+        system(command, '-echo');
 end
 
@@ -1859 +1892 @@
 if isfield(Param,'Pairs')
     Param=rmfield(Param,'Pairs'); %info Pairs not needed for output
+end
+if isfield(Param,'InputLine')
+    Param=rmfield(Param,'InputLine');
+end
+if isfield(Param,'EditObject')
+    Param=rmfield(Param,'EditObject');
 end
 Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
@@ -2328 +2367 @@
     SeriesData=get(handles.series,'UserData');
     % input line for which the field choice is relevant
-    iview=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));% all nc files, icluding civ
+    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'}));% all nc files, icluding civ
     hget_field=findobj(allchild(0),'name','get_field');
     if ~isempty(hget_field)
@@ -2337 +2376 @@
     % check the existence of the first file in the series
     first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1;%default setting for index j
-    if isfield(Param.IndexRange,'first_j');% if index j is used
+    if isfield(Param.IndexRange,'first_j');% if index j is used     
         first_j=Param.IndexRange.first_j;
         last_j=Param.IndexRange.last_j;
@@ -2346 +2385 @@
     if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
     [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
-    FirstFileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},...
-        InputTable{5},InputTable{4},i1,i2,j1,j2);
+    LineIndex=iview(1);
+    if numel(iview)>1      
+        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
+        LineIndex=str2num(answer);
+%         InputLine=str2num(get(handles.InputLine,'String'));
+%         if ismember(InputLine,iview)
+%             LineIndex=InputLine;
+%         end
+    end
+    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
+        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
     if exist(FirstFileName,'file')
         ParamIn.Title='get_field: pick input variables and coordinates for series processing';
@@ -2372 +2420 @@
                 XName='X';
                 YName='y';
-                set(handles.VelType,'visible','on')
-                set(handles.VelType_title,'visible','on')
         end
         set(handles.FieldName,'Value',1)
         set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
         if ~strcmp(GetFieldData.FieldOption,'civdata...')
-            set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
-            set(handles.VelType,'visible','off')
-            set(handles.VelType_title,'visible','off')
+           if ~isempty(regexp(FieldList{1},'^vec'))
+                set(handles.FieldName,'Value',1)
+           else
+                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
+           end
             XName=GetFieldData.Coordinates.Coord_x;
             YName=GetFieldData.Coordinates.Coord_y;
@@ -2392 +2440 @@
                     TimeName=['att:' GetFieldData.Time.TimeName];
                     % update the time table
-                    TimeTable{iview,2}=get_time(Param.IndexRange.MinIndex_i(iview),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % Min time     
-                    TimeTable{iview,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % first time              
-                    TimeTable{iview,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % last time                     
-                    TimeTable{iview,5}=get_time(Param.IndexRange.MaxIndex_i(iview),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % Max time
+                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
+                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time              
+                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
+                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
                 case 'variable'
                     set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
@@ -2409 +2457 @@
                     ParamIn.TimeDimName=GetFieldData.Time.TimeName;
             end
-            TimeTable{iview,1}=TimeName;
+            TimeTable{LineIndex,1}=TimeName;
             set(handles.TimeTable,'Data',TimeTable);
         end
         set(handles.Coord_x,'String',XName)
         set(handles.Coord_y,'String',YName)
+        set(handles.Coord_x,'Visible','on')
+        set(handles.Coord_y,'Visible','on')
     else
         msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
@@ -3106 +3156 @@
 ActionExtList=get(handles.ActionExt,'String');
 ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
-ActionList=get(handles.ActionName,'String');
-ActionName=ActionList{get(handles.ActionName,'Value')};
+if strcmp(ActionExt,'.py (in dev.)')
+    set(handles.RunMode,'Value',2)
+end
+% ActionList=get(handles.ActionName,'String');
+% ActionName=ActionList{get(handles.ActionName,'Value')};
 
 function num_NbProcess_Callback(hObject, eventdata, handles)

trunk/src/series/aver_stat.m

@@ -136 +136 @@
 for iview=1:NbView
     if ~exist(filecell{iview,1}','file')
-        msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'])
+        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
         return
     end
@@ -155 +155 @@
     diff_time=max(max(diff(time)));
     if diff_time>0
-        msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
+        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
     end   
 end
@@ -176 +176 @@
     FileExtOut='.nc';% write result as .nc files for netcdf inputs
 else
-    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
+    disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
     return
 end
 if NbView==2 && ~isequal(CheckImage{1},CheckImage{2})
-    msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
+    disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
     return
 end
@@ -216 +216 @@
 % index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
 nbfiles=0;
-nbmissing=0;
+% nbmissing=0;
 
 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
@@ -275 +275 @@
             [Field,errormsg]=proj_field(Field,Param.ProjObject);
             if ~isempty(errormsg)
-                msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg])
+                disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun)
                 return
             end
@@ -289 +289 @@
             DataOut=Field;%default
             DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files
-            for ivar=1:length(Field.ListVarName)
+            errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable
+            for ivar=1:numel(Field.ListVarName)
                 VarName=Field.ListVarName{ivar};
-                DataOut.(VarName)=double(DataOut.(VarName));
-            end
-        else   %current field
-            for ivar=1:length(Field.ListVarName)
-                VarName=Field.ListVarName{ivar};
-                sizmean=size(DataOut.(VarName));
-                siz=size(Field.(VarName));
-                if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
-                    disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
-                    return
+                DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
+                NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
+                for iivar=1:length(Field.VarAttribute)
+                    if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')...
+                            && strcmp(Field.VarAttribute{iivar}.Role,'errorflag')
+                        errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar
+                    end
+                end
+            end
+            DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result
+            DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result
+            DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result
+        end   %current field
+        for ivar=1:length(DataOut.ListVarName)
+            VarName=Field.ListVarName{ivar};
+            sizmean=size(DataOut.(VarName));
+            siz=size(Field.(VarName));
+            if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
+                disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
+                return
+            else
+                if errorvar(ivar)==0
+                    check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else
                 else
-                    DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
+                    check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else
                 end
+                Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
+                DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
+                NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point
             end
         end
@@ -315 +332 @@
 for ivar=1:length(Field.ListVarName)
     VarName=Field.ListVarName{ivar};
-    DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean
-end
+    DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean
+end
+nbmissing=NbField-nbfiles;
 if nbmissing~=0
-    msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'])
+    disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'],checkrun)
 end
 if isempty(time) % time is read from files

trunk/src/series/merge_proj.m

@@ -196 +196 @@
     FileExtOut='.nc'; %netcdf output
 end
-NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
+%NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
 RootFileOut=RootFile{1};
 for iview=2:NbView
@@ -403 +403 @@
 end
 errormsg='';
-MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field
+MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field
 NbView=length(Data);
-if NbView==1
-    return
+if NbView==1% if there is only one field, just reproduce it in MergeData
+    return 
 end
 
@@ -419 +419 @@
     if NbDim(icell)~=1 % skip field cells which are of dim 1
         switch CellInfo{icell}.CoordType
-            case 'scattered'  %case of input fields with unstructured coordinates: just concacene data
+            case 'scattered'  %case of input fields with unstructured coordinates: just concatene data
                 for ivar=CellInfo{icell}.VarIndex %  indices of the selected variables in the list FieldData.ListVarName
                     VarName=Data{1}.ListVarName{ivar};
-                    %MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field
                     for iview=2:NbView
                         MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
@@ -431 +430 @@
                 if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag)
                     FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable
+                    MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead)
+                    MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[];
+                    MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[];
                 end
                 % select good data on each view
@@ -441 +443 @@
                             check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else
                         end
-                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or masked data
+                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
                         if iview==1
-                            MergeData.(VarName)=Data{1}.(VarName);% correct the field of MergeData
+                            %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field
                             NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point
                         elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName))
                             errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object';
                             return
-                        else      
-                         
-                            MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName);%add data
+                        else                             
+                            MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data
                             NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else
                         end
                     end
                     MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point
+                    MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data
                 end
         end
-        if isempty(FFName)
-            FFName='FF';
-        end
-        MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data
-        MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data
+%         if isempty(FFName)
+%             FFName='FF';
+%         end
+%         MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data
+%         MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data
     end
 end

trunk/src/series/time_series.m

@@ -207 +207 @@
 %% Set field names and velocity types
 InputFields{1}=[];%default (case of images)
+if nbview==2
+    InputFields{2}=[];%default (case of images)
+end
 if isfield(Param,'InputFields')
     InputFields{1}=Param.InputFields;
-end
-if nbview==2
-    InputFields{2}=[];%default (case of images)
-    if isfield(Param,'InputFields')
-        InputFields{2}=Param.InputFields{1};%default
+    if nbview==2
+        InputFields{2}=Param.InputFields;%default
         if isfield(Param.InputFields,'FieldName_1')
             InputFields{2}.FieldName=Param.InputFields.FieldName_1;

trunk/src/uvmat.m

@@ -2818 +2818 @@
         elseif ref_j_1<0
             errormsg='minimum j index reached';
-        elseif ref_i_1+1>size(UvData.i1_series{2},3)
+        elseif ref_i_1+1>size(UvData.i1_series{2},3)&&~isempty(InputFile.NomType_1)
             errormsg='maximum i index reached for the second series (reload the input file to update the index bound)';
-        elseif ref_j_1+1>size(UvData.i1_series{2},2)
+        elseif ref_j_1+1>size(UvData.i1_series{2},2)&&~isempty(InputFile.NomType_1)
             errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
         end
@@ -2826 +2826 @@
         siz=size(UvData.i1_series{2});
         ref_indices=ref_i_1*siz(1)*siz(2)+ref_j_1*siz(1)+1:ref_i_1*siz(1)*siz(2)+(ref_j_1+1)*siz(1);
-        i1_subseries=UvData.i1_series{2}(ref_indices);
-        ref_indices=ref_indices(i1_subseries>0);
-        if isempty(ref_indices)% case of pairs (free index i)
-            ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2);
+        if ~isempty(InputFile.NomType_1)
             i1_subseries=UvData.i1_series{2}(ref_indices);
             ref_indices=ref_indices(i1_subseries>0);
-        end
-        i1_1=UvData.i1_series{2}(ref_indices(end));
-        if ~isempty(UvData.i2_series{2})
-            i2_1=UvData.i2_series{2}(ref_indices(end));
-        end
-        if ~isempty(UvData.j1_series{2})
-            j1_1=UvData.j1_series{2}(ref_indices(end));
-        end
-        if ~isempty(UvData.j2_series{2})
-            j2_1=UvData.j2_series{1}(ref_indices(end));
+            if isempty(ref_indices)% case of pairs (free index i)
+                ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2);
+                i1_subseries=UvData.i1_series{2}(ref_indices);
+                ref_indices=ref_indices(i1_subseries>0);
+            end
+            i1_1=UvData.i1_series{2}(ref_indices(end));
+            if ~isempty(UvData.i2_series{2})
+                i2_1=UvData.i2_series{2}(ref_indices(end));
+            end
+            if ~isempty(UvData.j1_series{2})
+                j1_1=UvData.j1_series{2}(ref_indices(end));
+            end
+            if ~isempty(UvData.j2_series{2})
+                j2_1=UvData.j2_series{1}(ref_indices(end));
+            end
         end
     else% the second series (if needed) is the same file as the first
@@ -3600 +3602 @@
 %% get bounds and dimensions of the input field
 UvData.Field=find_field_bounds(UvData.Field);
-
 testnewseries=UvData.NewSeries;
 UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)