Changeset 1194 for trunk

Timestamp:

Feb 23, 2026, 3:58:54 PM (8 days ago)

Author:

sommeria

Message:

several bugs repaired

Location:

trunk/src

Files:

• fill_GUI.m (modified) (3 diffs)
• find_file_series.m (modified) (5 diffs)
• get_field.fig (modified) (previous)
• get_field.m (modified) (10 diffs)
• nc2struct.m (modified) (1 diff)
• num2stra.m (modified) (2 diffs)
• read_multimadoc.m (modified) (1 diff)
• series.m (modified) (15 diffs)
• series/filter_time_singlefile.m (modified) (5 diffs)
• series/merge_proj.m (modified) (2 diffs)
• struct2nc.m (modified) (1 diff)

trunk/src/fill_GUI.m

@@ -33 +33 @@
 errormsg='';
 if ~isstruct(Param)
-    errormsg='first input parmaeter of fill_GUI must be a structure';
+    errormsg='first input parameter of fill_GUI must be a structure';
     return
 end
@@ -91 +91 @@
         end
         for ibox=1:numel(hh)
-        % finalise the update of GUI uicontrol filled by the input element
+            % finalise the update of GUI uicontrol filled by the input element
             if ~isempty(hh(ibox))&& ~check_done
                 set(hh(ibox),'Visible','on')% make the filled GUI element visible
@@ -104 +104 @@
                             if isnumeric(input_data)
                                 if numel(input_data)>0
-                                    input_string=num2str(input_data(ibox),4);
+                                    if floor(input_data(ibox))==input_data(ibox)
+                                        input_string=num2str(input_data(ibox)); % case of integers, write in full
+                                    else
+                                        input_string=num2str(input_data(ibox),4);%case of floating point:nbre_digit=4;
+                                    end
                                 end
                             elseif ischar(input_data)

trunk/src/find_file_series.m

@@ -1 +1 @@
 %'find_file_series': check the content of an input file and find the corresponding file series
 %--------------------------------------------------------------------------
-% function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,Object,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml)
+% function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,Object,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput)
 %
 % OUTPUT:
@@ -7 +7 @@
 % SubDir: data dir containing the input file series
 % RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file)
-% i1_series(pair,ref_j+1, ref_i+1),i2_series,j1_series,j2_series: set of indices (i1,i2,j1,j2) sorted by ref index ref_i, ref_j, and pairindex in case of multiple pairs with the same ref
-%  (ref_i+1 is used to deal with the image index zero sometimes used)
+% i1_series(pair,ref_j+1, ref_i+1): set of indices i1 sorted by ref index ref_i, ref_j, and pair index in case of multiple pairs with the same ref.
+%     (ref_i+1 is used to deal with the image index zero sometimes used)
+% i2_series,j1_series,j2_series: same as i1_series but for the indices i2,j1,j2.
+%  
 % NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string)
 % FileInfo: structure containing info on the input files (assumed identical on the whole series)
@@ -24 +26 @@
 % FilePath: path to the directory to be scanned
 % fileinput: name (without path) of the input file sample
-% checkxml: =1(default) take into account xml file existence to possibly include indexes in RootFile
-%           =0: do not take into account xml file existence
 
 %=======================================================================
@@ -45 +45 @@
 %=======================================================================
 
-function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml)
+function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput)
 %------------------------------------------------------------------------
 
@@ -75 +75 @@
         end
     else
-        %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file
-        if ~exist('checkxml','var')||checkxml
-            r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType
-            if ~isempty(r) %if NomType begins by a number or _1
-                fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
-                if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
-                    rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
-                else% if a separator '_' is  detected
-                    rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
-                end
-                if ~isempty(rr)
-                    RootFile_i=[RootFile rr.i1];% new root file
-                    %look for an xml file correspoonding to the new root name
-                    if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file'))
-                        RootFile=RootFile_i;
-                        NomTypePref=r.tiretnum;
-                        NomType=regexprep(NomType,['^'  NomTypePref],'');
-                        i1_input=j1_input;
-                        i2_input=j2_input;
-                        j1_input=[];
-                        j2_input=[];
-                    end
-                end
-            end
-        end
+     
         
         %% analyse the list of existing files when relevant

trunk/src/get_field.m

@@ -428 +428 @@
         pos(2)=pos_coord(2)-pos(4)-2;
         set(handles.PanelScalar,'Position',pos)
+        set(handles.Coord_x,'Visible','on')
         set(handles.Coord_y,'Visible','on')
         set(handles.Y_title,'Visible','on')     
@@ -507 +508 @@
 %------------------------------------------------------------------------
 Field=get(handles.get_field,'UserData');
-VarIndex=find(strcmp(VarName,Field.Display.ListVarName),1);
-DimCell=Field.Display.VarDimName{VarIndex};
+VarIndex=find(strcmp(VarName,Field.Display.ListVarName),1);% find the index of the input coord variable
+DimCell=Field.Display.VarDimName{VarIndex};% dimension(s) of the input coord variable
 
 
 %% set list of possible coordinates
-
-test_coord=zeros(size(Field.Display.VarDimName)); %=1 when variable #ilist is eligible as structured coordiante
-
-for ilist=1:numel(Field.Display.VarDimName)
-    %dimnames=Field.Display.VarDimName{ilist}; %list of dimensions for variable #ilist
-    % if isequal(dimnames,DimCell)||isequal(dimnames(1:end-1),DimCell)||isequal(dimnames(2:end),DimCell)
-    % if numel(dimnames)==1 || 
-    %     test_coord(ilist)=1;
-    % end
-end
-ListCoord=Field.Display.ListVarName;%(find(test_coord));
+if isequal(get(handles.FieldOption,'Value'),1)% case of 1D plot
+    test_coord=false(size(Field.Display.VarDimName)); %=true when variable #ilist is eligible as ordinate
+    for ilist=1:numel(Field.Display.VarDimName)
+        dimnames=Field.Display.VarDimName{ilist}; %list of dimensions for variable #ilist
+        if isequal(dimnames,DimCell)&& ~strcmp(Field.Display.ListVarName{ilist},VarName) %exclude the the same variable as coord_y
+            test_coord(ilist)=true;
+        elseif numel(dimnames)==2 && (isequal(dimnames(1),DimCell)||isequal(dimnames(2),DimCell))
+            test_coord(ilist)=true;
+        end
+    end
+    ListCoord=Field.Display.ListVarName(test_coord);
+else
+    ListCoord=Field.Display.ListVarName;
+end
 set(handles.Coord_y,'String',ListCoord)
 val_y=1;
@@ -605 +609 @@
 
 %% set list of possible coordinates
-test_component=zeros(size(Field.Display.VarDimName));%=1 when variable #ilist is eligible as unstructured coordinate
-test_coord=zeros(size(Field.Display.VarDimName)); %=1 when variable #ilist is eligible as structured coordiante
+test_component=false(size(Field.Display.VarDimName));%=1 when variable #ilist is eligible as unstructured coordinate
+test_coord=false(size(Field.Display.VarDimName)); %=1 when variable #ilist is eligible as structured coordiante
 dim_var=Field.Display.VarDimName{scalar_index};%list of dimensions of the selected variable
-%if ~get(handles.CheckDimensionX,'Value')
+
 %look for coordinate variables among the other variables
 for ilist=1:numel(Field.Display.VarDimName)
     dimnames=Field.Display.VarDimName{ilist}; %list of dimensions for variable #ilist
     if isequal(dimnames,dim_var)
-        test_component(ilist)=1;% the listed variable has the same dimension as the selected scalar-> possibly chosen as unstructured coordinate
+        test_component(ilist)=true;% the listed variable has the same dimension as the selected scalar-> possibly chosen as unstructured coordinate
     elseif numel(dimnames)==1 && ~isempty(find(strcmp(dimnames{1},dim_var), 1))%variable ilist is a 1D array which can be coordinate variable
-        test_coord(ilist)=1;
-    end
-end
-%end
+        test_coord(ilist)=true;
+%         if strcmp(dimnames{1},Field.Display.ListVarName{ilist})% case of diemnsion with same name as the variable
+%             test_select(ilist)=true
+    end
+end
+
 var_component=find(test_component);% list of variable indices elligible as unstructured coordinates
 var_coord=find(test_coord);% % list of variable indices elligible as gridded coordinates
-index_coord=[];
-index_component=[];
-for iscalar=1:numel(scalar_index)
-    index_component=[index_component find(var_component==scalar_index(iscalar),1)];
-    index_coord=[index_coord find(var_coord==scalar_index(iscalar),1)];
-end
-var_component(index_component)=[];
-var_coord(index_coord)=[];
+% index_coord=[];
+% index_component=[];
+% for iscalar=1:numel(scalar_index)
+%     index_component=[index_component find(var_component==scalar_index(iscalar),1)];
+%     index_coord=[index_coord find(var_coord==scalar_index(iscalar),1)];
+% end
+% var_component(index_component)=[];
+% var_coord(index_coord)=[];
 ListCoord=Field.Display.ListVarName([var_coord var_component]);
-coord_val=zeros(size(ListCoord));
+%coord_val=zeros(size(ListCoord));
 
 %% set default selection for grid coordinates
-if numel(var_coord)>=2
-    coord_val(1)=var_coord(end);
-    coord_val(2)=var_coord(end-1);
-    if numel(var_coord)>=3
-        coord_val(3)=var_coord(end-2);
-    end
-end
+% if numel(var_coord)>=2
+%     coord_val(1)=var_coord(end);
+%     coord_val(2)=var_coord(end-1);
+%     if numel(var_coord)>=3
+%         coord_val(3)=var_coord(end-2);
+%     end
+% end
 % if numel(find(test_coord))>3
 %     SwitchVarIndexTime=get(handles.SwitchVarIndexTime,'String');
@@ -649 +655 @@
 %     SwitchVarIndexTime_Callback([], [], handles)
 % end
+coord_val=[];
 
 %% default selection for labelled unstructured coordinates
@@ -664 +671 @@
     end
 end
-if numel(find(coord_val))<2 % no predefiend components
-    if numel(var_coord)>=3
-        coord_val(3)=3;
-    end
-    coord_val([1 2])=[1 2];
+% if numel(find(coord_val))<2 % no predefined components
+%     if numel(var_coord)>=3
+%         coord_val(3)=3;
+%     end
+%     coord_val([1 2])=[1 2];
+% end
+%% structured coordinates
+if isempty(coord_val)% structured coordinates
+    if numel(dim_var)>=3
+        ind_select3=find(strcmp(dim_var{3},ListCoord), 1);
+        if ~isempty(ind_select3)
+            coord_val(3)=ind_select3;
+        end
+    end
+    ind_select1=find(strcmp(dim_var{2},ListCoord));
+    if ~isempty(ind_select1)
+        coord_val(1)=ind_select1;
+    end
+    ind_select2=find(strcmp(dim_var{1},ListCoord));
+    if ~isempty(ind_select2)
+        coord_val(2)=ind_select2;
+    end
 end
 
@@ -676 +700 @@
 set(handles.Coord_y,'Value',coord_val(2))
 set(handles.Coord_y,'String',ListCoord)
-if numel(find(coord_val))>=3
+if numel(dim_var)>=3
     set(handles.Coord_z,'Value',coord_val(3))
     set(handles.Coord_z,'String',ListCoord)
@@ -882 +906 @@
 string=get(handles.Coord_x,'String');
 VarName=string{index};
-if ~ischar(DimCell)
-    update_field(handles,VarName)
+if ~ischar(DimCell)% no dimension as input
+    update_field(handles,VarName)% update the display of the variable 'VarName' and its dimensions in the general list of variables
 end
 if isequal(get(handles.FieldOption,'Value'),1)
-set_coord_y_options(handles,VarName)
+    set_coord_y_options(handles,VarName)
 end
 
@@ -899 +923 @@
 
 if ~ischar(DimCell)
-update_field(handles,VarName)
+    update_field(handles,VarName)
 end
 
@@ -911 +935 @@
 VarName=string{index};
 if ~ischar(DimCell)
-update_field(handles,VarName)
+    update_field(handles,VarName)
 end
 
@@ -1003 +1027 @@
 end
 
-
-
-% % --- Executes on button press in CheckDimensionY.
-% function CheckDimensionY_Callback(hObject, eventdata, handles)
-% FieldList=get(handles.FieldOption,'String');
-% FieldOption=FieldList{get(handles.FieldOption,'Value')};
-% switch FieldOption
-%     case '1D plot'
-%         
-%     case {'scalar','pick variables'}
-%        scalar_Callback(hObject, eventdata, handles)
-%     case 'vectors'
-% end
-% 
-% 
-% % --- Executes on button press in CheckDimensionZ.
-% function CheckDimensionZ_Callback(hObject, eventdata, handles)
-% FieldList=get(handles.FieldOption,'String');
-% FieldOption=FieldList{get(handles.FieldOption,'Value')};
-% switch FieldOption
-%     case '1D plot'
-%         
-%     case 'scalar'
-%        scalar_Callback(hObject, eventdata, handles)
-%     case 'vectors'
-% end
-
+%------------------------------------------------------------------------
 % --- Executes on selection change in TimeName.
+%------------------------------------------------------------------------
 function TimeName_Callback(hObject, eventdata, handles)
 

trunk/src/nc2struct.m

@@ -284 +284 @@
                     return
                 end
-                ind_vec(index_time)=TimeIndex-1;% selected index(or indices) to read
+                ind_vec(index_time)=TimeIndex(1)-1;% selected index(or indices) to read
                 ind_size(index_time)=numel(TimeIndex);%length of the selected set of time indices
                 if numel(TimeIndex)==1 && ~strcmp(VarName,TimeVarName)

trunk/src/num2stra.m

@@ -8 +8 @@
 % INPUT:
 % num: input number (file index)
-% nom_type: nomencalture type (see fct name_generator)
-% index: 1 or 2 (first or secodn index in file naming)
+% nom_type: nomenclature type (see fct name_generator)
+% index: 1 or 2 (first or second index in file naming)
 % see also: stra2num, name_generator, name2display
 
@@ -37 +37 @@
 switch index
     case 1
-%         if length(nom_type)>=4 && isequal(nom_type(1:2),'%0') && isequal(nom_type(4),'d') 
-%            str=num2str(num,nom_type(1:4)); 
-%         else
            str=num2str(num); 
-%         end
     case 2
         if ~isempty(nom_type) && (isequal(nom_type(end),'a')||isequal(nom_type(end),'b'))

trunk/src/read_multimadoc.m

@@ -79 +79 @@
 function time=get_time(timeimadoc,i1_series,i2_series,j1_series,j2_series)
  time=[];
- if ~ (isempty(i2_series)||size(timeimadoc,1) < i2_series(end) ||( ~isempty(j2_series) && size(timeimadoc,2) < j2_series(end)))% time array absent or too short in ImaDoc xml file'
+ if ~ (isempty(i2_series)||size(timeimadoc,1) < i2_series(end)+1 ||( ~isempty(j2_series) && size(timeimadoc,2) < j2_series(end)+1))% time array absent or too short in ImaDoc xml file'
      if isempty(j1_series)
          j1_series=1;

trunk/src/series.m

@@ -650 +650 @@
         j1=str2double(get(handles.num_first_j,'String'));
         j2=[];%default
-        PairString=get(handles.PairString,'Data');
-        if numel(PairString)>=iview
-            r=regexp(PairString{iview},'(?<num1>\d+)-(?<num2>\d+)' ,'names');
-            if ~isempty(r)
-                j1=str2double(r.num1);
-                j2=str2double(r.num2);
-            end
-        end
-        InputFile=fullfile_uvmat('','',InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1,[],j1,j2);
+%         PairString=get(handles.PairString,'Data');
+%         if numel(PairString)>=iview
+%             r=regexp(PairString{iview},'(?<num1>\d+)-(?<num2>\d+)' ,'names');
+%             if ~isempty(r)
+%                 j1=str2double(r.num1);
+%                 j2=str2double(r.num2);
+%             end
+%         end
+ InputFile=[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}];
+        %InputFile=fullfile_uvmat('','',InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1,[],j1,j2);
         [RootPath,~,RootFile,Param.i1_series,Param.i2_series,Param.j1_series,Param.j2_series,~,Param.FileInfo,MovieObject]=...
             find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),InputFile);
@@ -814 +815 @@
     SeriesData.j1_series={};
     SeriesData.j2_series={};
-    SeriesData.FileType={};
+ %   SeriesData.FileType={};
     SeriesData.FileInfo={};
     SeriesData.Time={};
@@ -1067 +1068 @@
 
     %% get index range in case of relabeling
-    if ~isempty(Param.XmlData.Time)
+    if isfield(Param,'XmlData') && ~isempty(Param.XmlData.Time)
         Time=Param.XmlData.Time;
         MinIndex_i=1;
@@ -1075 +1076 @@
         TimeName='xml';
     else
-        [nbfield,nbfield_j]=size(XmlData.Time);
+        InputTable=get(handles.InputTable,'Data');
+        [XmlFileName,Rank]=find_imadoc(InputTable{iview,1},InputTable{iview,2});
+        if isempty(XmlFileName)
+            return
+        else
+            Param.XmlData=read_imadoc(XmlFileName);
+        end
+        [nbfield,nbfield_j]=size(Param.XmlData.Time);
         nbfield=nbfield-1; %remove the possible index 0
         nbfield_j=nbfield_j-1; %remove the possible index 0
@@ -1089 +1097 @@
         %i1=(first_i-SeriesData.FileSeries{1}.FirstFileIndex)*SeriesData.FileSeries{1}.NbFramePerFile+1;%frame index deduced from input file index
         i1=1;
-        if strcmp(SeriesData.TimeName,'xml')% indices i and j
+        if isfield(SeriesData,'TimeName') && strcmp(SeriesData.TimeName,'xml')% indices i and j
             j1=mod(i1-1,nbfield_j)+first_j;
             i1=floor((i1-1)/nbfield_j)+1;
@@ -1096 +1104 @@
     end
 end
-%     set(handles.num_first_i,'String',num2str(i1))
-%     %         last_i=str2double(get(handles.num_last_i,'String'));
-%     %         last_j=str2double(get(handles.num_last_j,'String'));
-%     %         i1=(last_i-SeriesData.FileSeries{1}.FirstFileIndex)*SeriesData.FileSeries{1}.NbFramePerFile+1;%frame index deduced from input file index
-%     %         if strcmp(SeriesData.TimeName,'xml')% indices i and j
-%     %             j1=mod(i1-1,nbfield_j)+1;
-%     %             i1=floor((i1-1)/nbfield_j)+1;
-%     %         end
-%     set(handles.num_last_i,'String',num2str(nbfield))
-%     set(handles.num_last_j,'String',num2str(nbfield_j))
-% % else
-
-
-
-
-%     %% case of possible index relabeling from xml info
-%     if isfield(XmlData,'FileSeries')&& strcmp(FileInfo.FileType,'multimage')
-%         answer=msgbox_uvmat('INPUT_Y-N','relabel the frame  indices according to the xml info?');
-%         if strcmp(answer,'Yes')
-%             set(handles.Relabel,'Visible','on')
-%             set(handles.Relabel,'Value',1)
-%             SeriesData.FileSeries{iview}=XmlData.FileSeries;
-%             TimeMin=Time(2,2);
-%             TimeMax=Time(end,end);
-%             TimeFirst=TimeMin;
-%             TimeLast=TimeMax;
-%         end
-%     elseif iview==1
-%         set(handles.Relabel,'Visible','off')
-%     end
 
 if isfield(Param,'FileInfo') && ~isempty(Param.FileInfo) && strcmp(Param.FileInfo.FileType,'rdvision')
@@ -1137 +1115 @@
     end
     TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
-%     if size(Time)>=[first_i+1 first_j+1]
-%         TimeFirst=Time(first_i+1,first_j+1);
-%     end
-%     if size(Time)>=[last_i+1 last_j+1]
-%         TimeLast=Time(last_i+1,last_j+1);
-%     end
     if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1]
         TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
@@ -1261 +1233 @@
 CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
 PairString=get(handles.PairString,'Data');
+PairString{iview,1}=''; % no pair for #iview by default
 if CheckPair% if pairs need to be display for line iview
     [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
     Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),Param.FileInfo);
-    PairString{iview,1}=Menu{1};
-else
-    PairString{iview,1}=''; % no pair for #iview
+    if numel(Menu)>=1
+        PairString{iview,1}=Menu{1};
+    end
 end
 set(handles.PairString,'Data',PairString)
@@ -1282 +1255 @@
 Position=get(handles.FileStatus,'Position');
 set(handles.FileStatus,'Units','normalized')
-%xI=0.5:Position(3)-0.5;
 nbview=numel(SeriesData.i1_series);
-j_max=cell(1,nbview);
+i_max=cell(1,nbview);
 MaxIndex_i=ones(1,nbview); % default
 MinIndex_i=ones(1,nbview); % default
+missing_indices=cell(1,nbview);
 for iline=1:nbview
-    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
-    j_max{iline}=max(pair_max,[],1); % max on j index
-    if ~isempty(j_max{iline})
-        MaxIndex_i(iline)=find(j_max{iline}, 1, 'last' )-1; % max ref index i
-        MinIndex_i(iline)=find(j_max{iline}, 1 )-1; % min ref index i
+    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max i1 indices from i1_series (as obtained by fct uvmat/find_file_series.m)
+                                                            % needed in the case of mutiple pairs for the same index ref_i)
+    i_max{iline}=max(pair_max,[],1); % max on j index
+    if ~isempty(i_max{iline})&& ~isequal(pair_max,0)
+        MaxIndex_i(iline)=find(i_max{iline}, 1, 'last' )-1; % max ref index i
+        MinIndex_i(iline)=find(i_max{iline}, 1 )-1; % min ref index i
+         missing_indices{iline}= find(i_max{iline}(2:end)==0);          
     end
 end
@@ -1299 +1274 @@
 range_index=MaxIndex_i-MinIndex_i+1;
 range_y=max(1,floor(Position(4)/nbview));
-npx=floor(Position(3));
-file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
-CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
+npx=floor(Position(3));%length of the bar image FileStatus in pixels
+
+%file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
+CData=ones(nbview*range_y,npx); % initiate the image representing the existing files
+LineData=ones(1,npx);
 for iline=1:nbview
     ind_y=1+(iline-1)*range_y:iline*range_y;
-    LineData=zeros(size(file_indices));
-    file_select=file_indices(file_indices<=numel(j_max{iline}));
-    ind_select=file_indices<=numel(j_max{iline});
-    LineData(ind_select)=j_max{iline}(file_select)~=0;
-    CData(ind_y,:)=ones(size(ind_y'))*LineData;
+    missing_pixels=floor((missing_indices{iline}-MinIndex_i+1)*npx/range_index)+1;
+    LineData(missing_pixels)=0;
+%     LineData=zeros(size(file_indices));
+%     file_select=file_indices(file_indices<=numel(i_max{iline}));
+%     ind_select=file_indices<=numel(i_max{iline});
+%     LineData(ind_select)=i_max{iline}(file_select)~=0;
+    CData(ind_y,:)=ones(numel(ind_y),1)*LineData;%create an image band with width numel(ind_y)
 end
 CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
@@ -1520 +1499 @@
 if isempty(pos_last), pos_last=1; end
 Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
-Position_status=get(handles.FileStatus,'Position');
+Position_status=get(handles.FileStatus,'Position');% position of the FileStatus bar:= [ x,y, width, height]
 Position(1)=Position_status(1)+Position_status(3)*pos_first;
 Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
@@ -2642 +2621 @@
     end
     if  VelTypeRequest_1 && numel(iview_civ)>=2
-        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
+        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileInfo{iview_civ(2)}.FileType);
         set(handles.VelType_1,'Value',1)% set first choice by default
         set(handles.VelType_1,'String',[{'*'};menu])
@@ -2996 +2975 @@
     FieldListInit(field_index(1))=[];
     SeriesData=get(handles.series,'UserData');
+    for iview=1:numel(SeriesData.FileInfo)
+    FileType{iview}=SeriesData.FileInfo{iview}.FileType;
+    end
     % input line for which the field choice is relevant
-    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
+    iview=find(ismember(FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
     hget_field=findobj(allchild(0),'name','get_field');
     if ~isempty(hget_field)
@@ -3152 +3134 @@
     end
     Param=read_GUI(handles.series);
-    InputTable=Param.InputTable(2,:);
+    %InputTable=Param.InputTable(2,:);
     % check the existence of the first file in the series
     first_j=[];
@@ -4194 +4176 @@
 check_input_file_series(handles,CheckRelabel)
 ActionInput_Callback([],[], handles)
-% if get(handles.Relabel,'Value')
-%             NomType='*';
-%             i1=1;i2=[];j1=1;j2=[];
-%             i1_series=1:size(XmlData.Time,1)-1;    
-%             i2_series=[];
-%             j1_series=1:size(XmlData.Time,2)-1;
-%             j2_series=[];
-% 
-% 
-% 
-%     SeriesData=get(handles.series,'UserData');
-%     if isfield(SeriesData,'FileSeries')&& ~isempty(SeriesData.FileSeries{1})
-%         [nbfield,nbfield_j]=size(SeriesData.Time{1});
-%         nbfield=nbfield-1; %remove the possible index 0
-%         nbfield_j=nbfield_j-1; %remove the possible index 0
-%         MaxIndex_i=get(handles.MaxIndex_i,'Data');
-%         MaxIndex_j=get(handles.MaxIndex_j,'Data');
-%         MaxIndex_i(1,:)=nbfield;
-%         MaxIndex_j(1,:)=nbfield_j;
-%                 MinIndex_i(1,:)=1;
-%         MinIndex_j(1,:)=1;
-%         set(handles.MaxIndex_i,'Data',MaxIndex_i)
-%         set(handles.MaxIndex_j,'Data',MaxIndex_j)
-%          set(handles.MinIndex_i,'Data',MinIndex_i)
-%         set(handles.MinIndex_j,'Data',MinIndex_j)
-%         first_i=str2double(get(handles.num_first_i,'String'));
-%         first_j=str2double(get(handles.num_first_j,'String'));
-%         %i1=(first_i-SeriesData.FileSeries{1}.FirstFileIndex)*SeriesData.FileSeries{1}.NbFramePerFile+1;%frame index deduced from input file index
-%         i1=1;
-%         if strcmp(SeriesData.TimeName,'xml')% indices i and j
-%             j1=mod(i1-1,nbfield_j)+first_j;
-%             i1=floor((i1-1)/nbfield_j)+1;
-%             set(handles.num_first_j,'String',num2str(j1))
-%         end
-%         set(handles.num_first_i,'String',num2str(i1))
-% %         last_i=str2double(get(handles.num_last_i,'String'));
-% %         last_j=str2double(get(handles.num_last_j,'String'));
-% %         i1=(last_i-SeriesData.FileSeries{1}.FirstFileIndex)*SeriesData.FileSeries{1}.NbFramePerFile+1;%frame index deduced from input file index
-% %         if strcmp(SeriesData.TimeName,'xml')% indices i and j
-% %             j1=mod(i1-1,nbfield_j)+1;
-% %             i1=floor((i1-1)/nbfield_j)+1;
-% %         end
-%         set(handles.num_last_i,'String',num2str(nbfield))
-%          set(handles.num_last_j,'String',num2str(nbfield_j))
-%     end
-% else
-%     check_input_file_series(handles)
-%     ActionInput_Callback([],[], handles)
-% end
-
+
+

trunk/src/series/filter_time_singlefile.m

@@ -119 +119 @@
 % filecell{iview,fileindex}:
 %        iview: line in the table corresponding to a given file series
-%        fileindex: file index within  the file series, 
-% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j 
+%        fileindex: file index within  the file series,
+% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
 % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
 %%%%%%%%%%%% NbView=1 : a single input series
@@ -141 +141 @@
 [i1,~,j1,~] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
 [i2,~,j2,~] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
-ncfile_out=fullfile_uvmat(OutputPath,OutputDir,Param.InputTable{1,3},'.nc',NomTypeNc,i1,i2,j1,j2);
-
-% OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device));
-% RootFileOut=RootFile{1};
-% NomTypeOut='_1';
+ncfile_out=fullfile_uvmat(OutputPath,OutputDir,Param.InputTable{1,3},'*.nc',NomTypeNc,i1,i2,j1,j2);
 
 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
-disp('loop for filtering started')  
- ncid=[];
+disp('loop for filtering started')
+ncid=[];
 for index=1:NbField
     index
-   
     [Field,~,errormsg]= read_field(filecell{1,index},'netcdf',Param.InputFields);
     if ~isempty(errormsg)
         disp(errormsg)
         if ~isempty(ncid)
-        netcdf.close(ncid)
+            netcdf.close(ncid)
         end
         return
@@ -179 +174 @@
             VarDimIndex{ifield+3}=[2 3 1];
         end
-
-%         VarDimIndex={1,2,3,[1 2 3],[1 2 3]};
-
         DataOut.coord_x=Field.coord_x;
         DataOut.coord_y=Field.coord_y;
@@ -192 +184 @@
         netcdf.putVar(ncid,1,0,npy,Field.coord_y)
         netcdf.putVar(ncid,2,0,npx,Field.coord_x)
-%         Uvarid=3;
-%         Vvarid=4;
         TimeBlock=zeros(Param.ActionInput.WindowLength,1);
         Fieldblock=zeros(numel(ListFields),Param.ActionInput.WindowLength,npy,npx);
-        %Vblock=zeros(Param.ActionInput.WindowLength,npy,npx);
-    end
-
+    end
+    
     TimeBlock=circshift(TimeBlock,[-1 0 ]);
     TimeBlock(end)=Field.Time;
@@ -204 +193 @@
     Timefilter=mean(TimeBlock(end-sumindex:end,:,:));%mid time
     Fieldblock=circshift(Fieldblock,[0 -1 0 0]); %shift U by ishift along the first index
-   % Vblock=circshift(Vblock,[-1 0 0]); %shift U by ishift along the first index
     for ifield=1:numel(ListFields)
-    Fieldblock(ifield,end,:,:)=Field.(ListFields{ifield});
-    end
-    %Vblock(end,:,:)=Field.V;
+        Fieldblock(ifield,end,:,:)=Field.(ListFields{ifield});
+    end
     Fieldfilter=squeeze(mean(Fieldblock(:,end-sumindex:end,:,:),2,'omitnan'));
-%     Ufilter=squeeze(mean(Ublock(end-sumindex:end,:,:),1,'omitnan'));
-%     Vfilter=squeeze(mean(Vblock(end-sumindex:end,:,:),1,'omitnan'));
-%     Uerror=Ufilter-Ublock(end-floor(sumindex/2),:,:);
-%     Verror=Ufilter-Vblock(end-floor(sumindex/2),:,:);
-    %updating output the netcdf file
-     tstart = tic;
-    netcdf.putVar(ncid,0,(index-1),Timefilter)
+    netcdf.putVar(ncid,0,(index-1),Timefilter)    % update the field in the nc file
     for ifield=1:numel(ListFields)
         netcdf.putVar(ncid,Field_varid(ifield),[ 0 0 (index-1)],[npy npx 1],squeeze(Fieldfilter(ifield,:,:)))
     end
-%     netcdf.putVar(ncid,Uvarid,[ 0 0 (index-1)],[npy npx 1],Ufilter)
-%      netcdf.putVar(ncid,Vvarid,[0 0 (index-1)],[npy npx 1],Vfilter)
-
- telapsed = toc(tstart)% time for writting the field
-    % writing the result file as netcdf file
-    %     i1=i1_series{1}(index)-ceil(NpTime/2);
-    %     OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeOut,i1);
-    %     errormsg=struct2nc(OutputFile, DataOut);
-    %     if isempty(errormsg)
-    %         disp([OutputFile ' written'])
-    %     else
-    %         disp(errormsg)
-    %     end
-end
-netcdf.close(ncid)
-figure
-plot(telapsed)
-ylabel('time lapsed computation')
+end
+
 'END'

trunk/src/series/merge_proj.m

@@ -223 +223 @@
     NomTypeOut='_1_1';
 end
-%NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
 RootFileOut=RootFile{1};
 for iview=2:NbView
@@ -265 +264 @@
     if ~isempty(j1_series{1})
         j1=j1_series{1}(index);
-        if ~isempty(j2_series{end})
-            j2=j2_series{end}(index);
-        else
-            j2=j1;
-        end
-    end
-    OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1,i2,j1,j2);
+    end
+    i_out=floor((i1+i2)/2);
+    OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_out,[],j1);
     if ~CheckOverwrite && exist(OutputFile,'file')
             disp(['existing output file ' OutputFile ' already exists, skip to next field'])

trunk/src/struct2nc.m

@@ -68 +68 @@
 cmode = bitor(cmode, netcdf.getConstant('CLOBBER'));
 nc = netcdf.create(flname, cmode);
+netcdf.setFill(nc,'NOFILL')
 
 %% write global constants