Changeset 26


Ignore:
Timestamp:
Mar 2, 2010, 4:22:23 PM (11 years ago)
Author:
gostiaux
Message:

series native functions removed from series.m

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/src/series.m

    r25 r26  
    135135
    136136%loads the information stored in prefdir to initiate the browser and the list of functions
    137 menu_str=get(handles.ACTION,'String');%list of functions included in 'series.m'
    138 menu_str(end)=[];%remove from the list the last option 'more...'
    139 path_series=which('series');%path of the function 'series'
     137menu_str={'check_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'};
     138 
     139% menu_str=get(handles.ACTION,'String');%list of functions included in 'series.m'
     140
     141%remove from the list the last option 'more...'
     142[path_series,name,ext]=fileparts(which('series'));
     143path_series=fullfile(path_series,'/series');%path of the function 'series'
     144
    140145for ilist=1:length(menu_str)
    141146    fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m'
     
    151156             menu_str=[menu_str; {file}];
    152157         end
    153          menu_str=[menu_str;{'more...'}];
    154          set(handles.ACTION,'String',menu_str)
    155     end
    156 end
     158    end
     159end
     160
     161menu_str=[menu_str;{'more...'}];
     162set(handles.ACTION,'String',menu_str)
    157163set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION
    158164
     
    14811487    end
    14821488end
     1489% fct_path
     1490        eval(['h_fun=@' action])
     1491if ~isequal(fct_path,path_series)
     1492        rmpath(fct_path)% add the prescribed path if not the current one   
     1493end
     1494
    14831495Series.Action=action;%name of the processing programme
    14841496set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
    14851497drawnow
    14861498if length(RootPath)>1
    1487     feval(action,num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series);
     1499%    feval(action,num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series);
     1500    h_fun(num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series);
    14881501else
    1489     feval(action,num_i1,num_i2,num_j1,num_j2,Series);
     1502    h_fun(num_i1,num_i2,num_j1,num_j2,Series);
     1503%     feval(action,num_i1,num_i2,num_j1,num_j2,Series);
    14901504end
    14911505set(handles.RUN,'BackgroundColor',[1 0 0])
     
    16111625end
    16121626if nb_builtin==0% the path of series has been changed, reinitialize
    1613     series_OpeningFcn(hObject, eventdata, handles)
     1627%     series_OpeningFcn(hObject, eventdata, handles)
    16141628    return
    16151629end
     
    16181632if isequal(ACTION,'more...')
    16191633    pathfct=fileparts(path_series);
    1620     browse_name=fullfile(path_series,'SERIES_FCT');%go to UVMAT/SERIES_FCT by default
     1634    browse_name=fullfile(path_series,'series');%go to UVMAT/SERIES_FCT by default
    16211635    if length(list_path)>nb_builtin
    16221636        browse_name=list_path{end};% initialize browser with  the path of the last introduced function
     
    16301644        return
    16311645    end
    1632     ext_fct=FileName(end-1:end);
     1646   
     1647   
     1648   
     1649    ext_fct=FileName(end-1:end);% to be replaced by fileparts
    16331650    if ~isequal(ext_fct,'.m')
    16341651        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
     
    16361653    end
    16371654    ACTION=FileName(1:end-2);% ACTION choice updated by the selected item
     1655   
     1656    addpath(PathName)
     1657    eval(['h_function=@' ACTION]);
     1658    if ~isequal(path_series,PathName)
     1659    rmpath(PathName)
     1660    end
     1661    functions(h_function)
    16381662   
    16391663   % insert the choice in the action menu
     
    18951919     update_menu(handles.FieldMenu_1,scalar)
    18961920end   
    1897 
    1898 
    1899 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    1900  %detect the chosen series of files and check their date of modification:
    1901 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    1902 %INPUT:
    1903 %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    1904 %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    1905 %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
    1906 %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
    1907 %OTHER INPUTS given by the structure Series
    1908 function GUI_input=check_files(num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series) %(filecell,filecell_1,num_i,num_j,vel_type,field,param);
    1909 
    1910 %requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
    1911 if ~exist('num_i1_cell','var')
    1912     GUI_input={'RootPath';'many';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
    1913         'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
    1914         'RootFile';'on';... %root input file name ('on' by default)
    1915         'FileExt';'on';... %input file extension ('on' by default)
    1916         'NomType';'on';...%type of file indexing ('on' by default)
    1917         'NbSlice';'on'; ...%nbre of slices ('off' by default)
    1918         %'VelTypeMenu';'on';...% menu for selecting the velocity type (civ1,..) 'off' by default)
    1919         %'FieldMenu';'on';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
    1920         %'CoordType';'on'...%can use a transform function 'off' by default
    1921         %'GetObject';'on'...%can use projection object ,'off' by default
    1922         %'GetMask';'on'...%can use mask option   ,'off' by default
    1923         %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter
    1924                ''};
    1925     return %exit the function
    1926 end
    1927 
    1928 %standard parameters for waitbar and STOP action (do not modify)
    1929 hseries=guidata(Series.hseries);%handles of the GUI series
    1930 WaitbarPos=get(hseries.waitbar_frame,'Position');
    1931 
    1932 %%%%%%%%%%%%%%%%%%%%%%%%
    1933 
    1934 % number of slices
    1935 NbSlice=str2num(get(hseries.NbSlice,'String'));
    1936 if isempty(NbSlice)
    1937     NbSlice=1;
    1938 end
    1939 NbSlice_name=num2str(NbSlice);
    1940 if isequal(NbSlice,[]),NbSlice=1; end; %default
    1941 
    1942 % number of views
    1943 count=0;
    1944 testcell=iscell(Series.RootFile);
    1945 if ~testcell
    1946     Series.RootPath={Series.RootPath};
    1947     Series.RootFile={Series.RootFile};
    1948     Series.SubDir={Series.SubDir};
    1949     Series.FileExt={Series.FileExt};
    1950     Series.NomType={Series.NomType};
    1951 end   
    1952 nbview=length(Series.RootFile);
    1953 for iview=1:nbview
    1954     filebase=fullfile(Series.RootPath{iview},Series.RootFile{iview});%root file name
    1955     if testcell
    1956         num_i1=num_i1_cell{iview}; num_i2=num_i2_cell{iview}; num_j1=num_j1_cell{iview}; num_j2=num_j2_cell{iview};
    1957     else
    1958         num_i1=num_i1_cell; num_i2=num_i2_cell; num_j1=num_j1_cell; num_j2=num_j2_cell;
    1959     end
    1960     siz=size(num_i1);
    1961     nbfield2=siz(1); %nb of consecutive fields at each level(burst
    1962     nbfield=siz(1)*siz(2);
    1963     nbfield=floor(nbfield/(nbfield2*NbSlice));%total number of i indexes (adjusted to an integer number of slices)
    1964     if isequal(lower(Series.FileExt{iview}),'.avi')
    1965         info=aviinfo([filebase Series.FileExt{iview}]);
    1966         message{1}=info.Filename;
    1967         message{2}=info.FileModDate;
    1968         message{3}=[num2str(info.FramesPerSecond) ' frames/s '];
    1969         message{4}=info.ImageType;
    1970         message{5}=['  compression' info.VideoCompression];
    1971         message{6}=[ 'quality ' num2str(info.Quality)];   
    1972         Tabchar=message;
    1973     else
    1974         datnum=[];
    1975         Tabchar={};
    1976         %LOOP ON SLICES
    1977         for i_slice=1:NbSlice
    1978             for ifield=1:nbfield
    1979                 indselect(:,ifield)=((ifield-1)*NbSlice+(i_slice-1))*nbfield2+[1:nbfield2]';%selected indices on the list of files of a slice
    1980             end
    1981             for index=1:nbfield*nbfield2
    1982                 stopstate=get(hseries.RUN,'BusyAction');
    1983                 if isequal(stopstate,'queue')% enable STOP command
    1984                     update_waitbar(hseries.waitbar,WaitbarPos,index/(nbfield*nbfield2))
    1985                     ifile=indselect(index);               
    1986                     file=...
    1987                        name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2(ifile),num_j2(ifile),Series.SubDir{iview});               
    1988                     [Path,Name,ext]=fileparts(file);
    1989                     detect=exist(file,'file'); % check the existence of the file
    1990                     if detect==0
    1991                         count=count+1;
    1992                         lastfield='not found';
    1993                     else
    1994                         datfile=dir(file);
    1995                         datnum(ifile)=datenum(datfile.date);
    1996                         filefound(ifile)={datfile.name};
    1997                         lastfield='';
    1998                         if isequal(Series.FileExt{iview},'.nc') || isequal(Series.FileExt{iview},'.cdf')
    1999                             % check the content  netcdf file
    2000                             Data=nc2struct(file,'ListGlobalAttribute','patch2','fix2','civ2','patch','fix','absolut_time_T0','hart');
    2001                             if ~isempty(Data.patch2) && isequal(Data.patch2,1)
    2002                                 lastfield='patch2';
    2003                             elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
    2004                                 lastfield='fix2';
    2005                             elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
    2006                                 lastfield='civ2';
    2007                             elseif ~isempty(Data.patch) && isequal(Data.patch,1);
    2008                                 lastfield='patch1';
    2009                             elseif ~isempty(Data.fix) && isequal(Data.fix,1);
    2010                                 lastfield='fix1';
    2011                             elseif ~isempty(Data.absolut_time_T0) && ~isempty(Data.hart)
    2012                                 lastfield='civ1';
    2013                             end                         
    2014                         end
    2015                     end
    2016                     Tabchar(1,i_slice)={['slice #' num2str(i_slice)]};
    2017                     Tabchar(index+1,i_slice)={[file '   ' lastfield]};
    2018                 end
    2019             end
    2020         end
    2021         if isempty(datnum)
    2022             if NbSlice>1
    2023                 message=['no set of ' num2str(NbSlice) ' (NbSlices) files found'];
    2024             else
    2025                  message='no file found';
    2026             end
    2027         else
    2028             datnum=datnum(find(datnum));%keep the non zero values corresponding to existing files
    2029             [first,ind]=min(datnum);
    2030             [last,indlast]=max(datnum);
    2031             message={['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
    2032                 ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
    2033         end
    2034         if ~isempty(Tabchar)
    2035           Tabchar=reshape(Tabchar,NbSlice*(nbfield*nbfield2+1),1);
    2036         end
    2037     end
    2038     hfig=figure(iview);
    2039     clf
    2040     if iview>1
    2041         pos=get(iview-1,'Position');
    2042         pos(1)=pos(1)+(iview-1)*pos(1)/nbview;
    2043         set(hfig,'Position',pos)
    2044     end
    2045     set(hfig,'name',['view= ' num2str(iview)])
    2046    
    2047     h=uicontrol('Style','listbox', 'Position', [20 20 500 300], 'String', Tabchar, 'Callback', @ncbrowser_uvmat);
    2048     hh=uicontrol('Style','listbox', 'Position', [20 340 500 40], 'String', message);
    2049 end
    2050 %----------------------------------------------------
    2051 %  determine the list of index pairs of processing file
    2052 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    2053 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)
    2054 num_i1=num_i;% set of first image numbers by default
    2055 num_i2=num_i;
    2056 num_j1=num_j;
    2057 num_j2=num_j;
    2058 num_i_out=num_i;
    2059 num_j_out=num_j;
    2060 if isequal (NomType,'_i1-i2_j') |isequal (NomType,'_i1-i2')
    2061     num_i1_line=num_i+ind_shift(3);% set of first image numbers
    2062     num_i2_line=num_i+ind_shift(4);
    2063     % adjust the first and last field number
    2064         indsel=find(num_i1_line >= 1);
    2065     num_i_out=num_i(indsel);
    2066     num_i1_line=num_i1_line(indsel);
    2067     num_i2_line=num_i2_line(indsel);
    2068     num_j1=meshgrid(num_j,ones(size(num_i1_line)));
    2069     num_j2=meshgrid(num_j,ones(size(num_i1_line)));
    2070     [xx,num_i1]=meshgrid(num_j,num_i1_line);
    2071     [xx,num_i2]=meshgrid(num_j,num_i2_line);
    2072 elseif isequal (NomType,'_i_j1-j2') || isequal (NomType,'#_ab')
    2073     if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
    2074         num_j1=ind_shift(1)*ones(size(num_i));
    2075         num_j2=ind_shift(2)*ones(size(num_i));
    2076     else
    2077         num_j1_col=num_j+ind_shift(1);% set of first image numbers
    2078         num_j2_col=num_j+ind_shift(2);
    2079         % adjust the first field number
    2080         indsel=find((num_j1_col >= 1));   
    2081         num_j_out=num_j(indsel);
    2082         num_j1_col=num_j1_col(indsel);
    2083         num_j2_col=num_j2_col(indsel);
    2084         [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
    2085         [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
    2086     end   
    2087 end
    2088 
    2089 
    2090 %----------------------------------------------------------------------
    2091 % --- make average on a series of files
    2092 %----------------------------------------------------------------------
    2093 %INPUT:
    2094 %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    2095 %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    2096 %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
    2097 %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
    2098 %OTHER INPUTS given by the structure Series
    2099 %  Series.Time:
    2100 %  Series.GeometryCalib:
    2101 function GUI_input=aver_stat(num_i1,num_i2,num_j1,num_j2,Series)
    2102 %requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
    2103 if ~exist('num_i1','var')
    2104     GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
    2105         'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
    2106         'RootFile';'on';... %root input file name ('on' by default)
    2107         'FileExt';'on';... %input file extension ('on' by default)
    2108         'NomType';'on';...%type of file indexing ('on' by default)
    2109         'NbSlice';'on'; ...%nbre of slices ('off' by default)
    2110         'VelTypeMenu';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
    2111         'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
    2112         'CoordType'; 'on';...%can use a transform function
    2113         'GetObject';'on';...%can use projection object(option 'off'/'one'/'two',
    2114         %'GetMask';'on'...%can use mask option   
    2115         %'PARAMETER'; %options: name of the user defined parameter',repeat a line for each parameter
    2116                ''};
    2117         return
    2118 end
    2119 
    2120 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    2121 hseries=guidata(Series.hseries);%handles of the GUI series
    2122 WaitbarPos=get(hseries.waitbar_frame,'Position');
    2123 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    2124 
    2125 %root input file and type
    2126 if ~iscell(Series.RootPath)% case of a single input field series
    2127     num_i1={num_i1};num_j1={num_j1};num_i2={num_i2};num_j2={num_j2};
    2128     RootPath={Series.RootPath};
    2129     RootFile={Series.RootFile};
    2130     SubDir={Series.SubDir};
    2131     FileExt={Series.FileExt};
    2132     NomType={Series.NomType};
    2133 else
    2134     RootPath=Series.RootPath;
    2135     RootFile=Series.RootFile;
    2136     SubDir=Series.SubDir;
    2137     NomType=Series.NomType;
    2138     FileExt=Series.FileExt;
    2139 end   
    2140 ext=FileExt{1};
    2141 form=imformats(ext([2:end]));%test valid Matlab image formats
    2142 testima=0;
    2143 if ~isempty(form)||isequal(lower(ext),'.avi')||isequal(lower(ext),'.vol')
    2144     testima(1)=1;
    2145 end
    2146 if length(FileExt)>=2
    2147     ext_1=FileExt{2};
    2148     form=imformats(ext_1([2:end]));%test valid Matlab image formats
    2149     if ~isempty(form)||isequal(lower(ext_1),'.avi')||isequal(lower(ext_1),'.vol')
    2150         testima(2)=1;
    2151     end
    2152     if testima(2)~=testima(1)
    2153         msgbox_uvmat('ERROR','images and netcdf files cannot be compared')
    2154         return
    2155     end
    2156 end
    2157 
    2158 %Number of input series: this function  accepts two input file series at most (then it operates on the difference of fields)
    2159 nbview=length(RootPath);
    2160 if nbview>2 
    2161     RootPath=RootPath(1:2);
    2162     set(hseries.RootPath,'String',RootPath)
    2163     SubDir=SubDir(1:2);
    2164     set(hseries.SubDir,'String',SubDir)
    2165     RootFile=RootFile(1:2);
    2166     set(hseries.RootFile,'String',RootFile)
    2167     NomType=NomType(1:2);
    2168     FileExt=FileExt(1:2);
    2169     set(hseries.FileExt,'String',FileExt)
    2170     nbview=2;
    2171 end
    2172 hhh=which('mmreader');
    2173 for iview=1:nbview
    2174     test_movie(iview)=0;
    2175     if ~isequal(hhh,'')&& mmreader.isPlatformSupported()
    2176         if isequal(lower(FileExt{iview}),'.avi')
    2177             MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}]));
    2178             test_movie(iview)=1;
    2179         end
    2180     end
    2181 end
    2182 
    2183 % number of slices
    2184 NbSlice=str2num(get(hseries.NbSlice,'String'));
    2185 if isempty(NbSlice)
    2186     NbSlice=1;
    2187 end
    2188 NbSlice_name=num2str(NbSlice);
    2189 
    2190 % Field and velocity type (the same for the two views)
    2191 Field_str=get(hseries.FieldMenu,'String');
    2192 FieldName=[]; %default
    2193 testfield=get(hseries.FieldMenu,'Visible');
    2194 if isequal(testfield,'on')
    2195     val=get(hseries.FieldMenu,'Value');
    2196     FieldName=Field_str(val);%the same set of fields for all views
    2197     if isequal(FieldName,{'get_field...'})
    2198         hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
    2199         if length(hget_field)>1
    2200             delete(hget_field(2:end))
    2201         elseif isempty(hget_field)
    2202            filename=...
    2203                  name_generator(fullfile(RootPath{1},RootFile{1}),num_i1{1}(1),num_j1{1}(1),FileExt{1},NomType{1},1,num_i2{1}(1),num_j2{1}(1),SubDir{1});
    2204            get_field(filename);
    2205            return
    2206         end
    2207         %hhget_field=guidata(hget_field);%handles of GUI elements in get_field
    2208         SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
    2209     end
    2210 end
    2211 %detect whether the two files are 'images' or 'netcdf'
    2212 testima=0;
    2213 testvol=0;
    2214 testcivx=0;
    2215 testnc=0;
    2216 FileExt=get(hseries.FileExt,'String');
    2217 % test_movie=0;
    2218 for iview=1:nbview
    2219      ext=FileExt{iview};
    2220      form=imformats(ext([2:end]));
    2221      if isequal(lower(ext),'.vol')
    2222          testvol=testvol+1;
    2223      elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab
    2224          testima=testima+1;
    2225      elseif isequal(ext,'.nc')
    2226          testnc=testnc+1;
    2227      end
    2228 end
    2229 if testvol
    2230     msgbox_uvmat('ERROR','volume images not implemented yet')
    2231     return
    2232 end
    2233 if testnc~=nbview && testima~=nbview && testvol~=nbview
    2234     msgbox_uvmat('ERROR','compare two image series or two netcdf files with the same fields as input')
    2235     return
    2236 end
    2237 if ~isequal(FieldName,{'get_field...'})
    2238     testcivx=testnc;
    2239 end
    2240 
    2241 if testcivx
    2242     VelType_str=get(hseries.VelTypeMenu,'String');
    2243     VelType_val=get(hseries.VelTypeMenu,'Value');
    2244     VelType{1}=VelType_str{VelType_val};
    2245     if nbview==2
    2246         VelType_str=get(hseries.VelTypeMenu_1,'String');
    2247         VelType_val=get(hseries.VelTypeMenu_1,'Value');
    2248         VelType{2}=VelType_str{VelType_val};
    2249     end
    2250 end
    2251 
    2252 %Calibration data and timing: read the ImaDoc files
    2253 mode=''; %default
    2254 timecell={};
    2255 itime=0;
    2256 NbSlice_calib={};
    2257 for iview=1:nbview%Loop on views
    2258     XmlData{iview}=[];%default
    2259     filebase{iview}=fullfile(RootPath{iview},RootFile{iview});
    2260     if exist([filebase{iview} '.xml'],'file')
    2261         [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']);
    2262         if isfield(XmlData{iview},'Time')
    2263             itime=itime+1;
    2264             timecell{itime}=XmlData{iview}.Time;
    2265         end
    2266         if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord')
    2267             NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
    2268             if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
    2269                 msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
    2270             end
    2271         end
    2272     elseif exist([filebase{iview} '.civ'],'file')
    2273         [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']);
    2274         itime=itime+1;
    2275         timecell{itime}=time;
    2276         XmlData{iview}.Time=time;
    2277         GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
    2278         GeometryCalib.Tx=0;
    2279         GeometryCalib.Ty=0;
    2280         GeometryCalib.Tz=1;
    2281         GeometryCalib.dpx=1;
    2282         GeometryCalib.dpy=1;
    2283         GeometryCalib.sx=1;
    2284         GeometryCalib.Cx=0;
    2285         GeometryCalib.Cy=0;
    2286         GeometryCalib.f=1;
    2287         GeometryCalib.kappa1=0;
    2288         GeometryCalib.CoordUnit='cm';
    2289         XmlData{iview}.GeometryCalib=GeometryCalib;
    2290         if error==1
    2291             msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
    2292         end
    2293     end
    2294 end
    2295 
    2296 %check coincidence in time
    2297 multitime=0;
    2298 if length(timecell)==0
    2299     time=[];
    2300 elseif length(timecell)==1
    2301     time=timecell{1};
    2302 elseif length(timecell)>1
    2303     multitime=1;
    2304     for icell=1:length(timecell)
    2305         if ~isequal(size(timecell{icell}),size(timecell{1}))
    2306             msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used')
    2307             time=timecell{1};
    2308             multitime=0;
    2309             break
    2310         end
    2311     end
    2312 end
    2313 if multitime
    2314     for icell=1:length(timecell)
    2315         time(icell,:,:)=timecell{icell};
    2316     end
    2317     diff_time=max(max(diff(time)));
    2318     if diff_time>0
    2319         msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)])
    2320     end   
    2321 end
    2322 if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file'
    2323     time=[];
    2324 end
    2325 
    2326 % Root name of output files (TO GENERALISE FOR TWO INPUT SERIES)
    2327 filebasesub=fullfile(RootPath{1},SubDir{1},RootFile{1});
    2328 if isempty(SubDir{1}) % create a subdirectory '/mean'
    2329     subdir_result='mean';
    2330 %     filebasemean=fullfile(RootPath{1},subdir_result);
    2331     if ~exist(fullfile(RootPath{1},subdir_result),'dir')
    2332         dircur=pwd; %record current working directory
    2333         cd(RootPath{1})% goes to the iamge directory
    2334         [m1,m2,m3]=mkdir(subdir_result);
    2335         if ~isequal(m2,'')
    2336              msgbox_uvmat('CONFIRMATION',m2);%error message for directory creation
    2337         end
    2338         cd(dircur) %back to the initial working directory
    2339     end
    2340     filebase_out=filebase{1};
    2341 else
    2342    subdir_result=SubDir{1};
    2343    filebase_out=[filebase{1} '_mean'];% output root name obtained by adding the suffix _mean to the input
    2344 end
    2345 %output nomtype (to generalise)
    2346 NomTypeOut=nomtype2pair(NomType{1},num_i2{end}(end)-num_i1{1}(1),num_j2{end}(end)-num_j1{1}(1));
    2347    
    2348 if NbSlice==1 
    2349     filebase_out=[filebasesub '_mean'];
    2350 else
    2351     filebase_out=[filebasesub '_' NbSlice_name 'mean'];
    2352     answeryes=questdlg({['will make average in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_out ' ...']});
    2353     if ~isequal(answeryes,'Yes')
    2354         return
    2355     end
    2356 end
    2357 
    2358 % coordinate transform or other user defined transform
    2359 Coord_menu=get(hseries.CoordType,'String');
    2360 menu_val=get(hseries.CoordType,'Value');
    2361 usrfct=Coord_menu{menu_val};
    2362 testfct=~isequal(usrfct,'');
    2363 
    2364 %slice loop
    2365 siz=size(num_i1{1});
    2366 lengthtot=siz(1)*siz(2);
    2367 nbfield=floor(lengthtot/(siz(1)*NbSlice));%total number of i indexes (adjusted to an integer number of slices)
    2368 nbfield_slice=nbfield*siz(1);% number of fields per slice
    2369 
    2370 for i_slice=1:NbSlice
    2371    S=0; %initiate the image sum S
    2372    nbfiles=0;
    2373    nbmissing=0;
    2374     %averaging loop
    2375    for ifile=i_slice:NbSlice:lengthtot
    2376         stopstate=get(hseries.RUN,'BusyAction');
    2377         if isequal(stopstate,'queue') % enable STOP command
    2378              update_waitbar(hseries.waitbar,WaitbarPos,ifile/lengthtot)
    2379              for iview=1:nbview
    2380                 [filename]=...
    2381                            name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),FileExt{iview},NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview});
    2382                 if testima
    2383                     Data{iview}.ListVarName={'A'};
    2384                     Data{iview}.AName='image';
    2385                     if test_movie(iview)
    2386                         Data{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile));
    2387                     else
    2388                         Data{iview}.A=read_image(filename,NomType{iview},num_i1{iview}(ifile));% read the image, num2 is the counter for avi files
    2389                     end
    2390                     Atype{iview}=class(Data{iview}.A);
    2391                     Data{iview}.A=double(Data{iview}.A);
    2392                 elseif testcivx
    2393                     [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType);
    2394                 else
    2395                     [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data               
    2396                     Data{iview}.VarAttribute=SubField.VarAttribute;
    2397                 end
    2398                 if isfield(Data{iview},'Txt')
    2399                     msgbox_uvmat('ERROR',['error of input reading: ' Data{iview}.Txt])
    2400                     return
    2401                 end
    2402              end   
    2403              % coordinate transform (or other user defined transform)
    2404              if ~isequal(Series.CoordType,'')
    2405                  % z index
    2406                 if ~isempty(NbSlice_calib)
    2407                     Data{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1;%Zindex for phys transform
    2408                 end
    2409                 if nbview==2
    2410                     [Data{1},Data{2}]=feval(Series.CoordType,Data{1},XmlData{1},Data{2},XmlData{2});
    2411                     if isempty(Data{2})
    2412                         Data(2)=[];
    2413                     end
    2414                 else
    2415                     Data{1}=feval(Series.CoordType,Data{1},XmlData);
    2416                 end
    2417              end     
    2418             if testcivx
    2419                     Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..)
    2420             end
    2421             if length(Data)==2
    2422                 [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields
    2423                 if ~isempty(errormsg)
    2424                     msgbox_uvmat('ERROR',['error in aver_stat/sub_field:' errormsg])
    2425                     return
    2426                 end
    2427             else
    2428                 Field=Data{1};
    2429             end
    2430             if isfield(Series,'ProjObject')
    2431                 [Field,errormsg]=proj_field(Field,Series.ProjObject);
    2432                  if ~isempty(errormsg)
    2433                     msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg])
    2434                     return
    2435                 end
    2436              end                                                       
    2437                 nbfiles=nbfiles+1;
    2438                 if nbfiles==1 %first field
    2439                     time_1=[];
    2440                     if isfield(Field,'Time')
    2441                         time_1=Field.Time(1);
    2442                     end
    2443                     DataMean=Field;%default
    2444                 else
    2445                     for ivar=1:length(Field.ListVarName)
    2446                         VarName=Field.ListVarName{ivar};
    2447                         eval(['sizmean=size(DataMean.' VarName ');']);
    2448                         eval(['siz=size(Field.' VarName ');']);
    2449                         if ~isequal(siz,sizmean)
    2450                             warndlg_uvmat(['unequal size of input field ' VarName ', need to interpolate on a grid'],'WARNING')
    2451                             nbmissing=nbmissing+1;
    2452                             break
    2453                         else
    2454                             eval(['DataMean.' VarName '=DataMean.' VarName '+ Field.' VarName ';']); % update the sum
    2455                         end
    2456                     end
    2457                 end
    2458 %             else
    2459 %                 nbmissing=nbmissing+1;
    2460 %             end
    2461         end
    2462     end %end averaging loop
    2463     for ivar=1:length(Field.ListVarName)
    2464         VarName=Field.ListVarName{ivar};
    2465         eval(['DataMean.' VarName '=DataMean.' VarName '/nbfiles;']); % normalize the mean
    2466     end
    2467     if nbmissing~=0
    2468         msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'])
    2469     end
    2470     if isempty(time) % time read from files  prevails
    2471         time_end=[];
    2472         if isfield(Field,'Time')
    2473             time_end=Field.Time(1);%last time read
    2474             if ~isempty(time_1)
    2475                 DataMean.Time=time_1;
    2476                 DataMean.Time_end=time_end;
    2477             end
    2478         end
    2479     else  % time from ImaDoc prevails
    2480         DataMean.Time=time(1,num_i1{1}(1),num_j1{1}(1));
    2481         DataMean.Time_end=time(end,num_i1{end}(end),num_j1{end}(end));
    2482     end
    2483    
    2484     %writing the result file
    2485    if testima   
    2486        if NbSlice==1
    2487         [filemean]=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.png',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end));
    2488        else % label the file number by the slice # for simplicity
    2489           [filemean]=name_generator(filebase_out,i_slice,1,'.png','_i');
    2490        end
    2491         if exist(filemean,'file')
    2492             backupfile=filemean;
    2493             testexist=2;
    2494             while testexist==2
    2495                 backupfile=[backupfile(1:end-4) '~.png'];
    2496                 testexist=exist(backupfile,'file');
    2497             end
    2498             [success,message]=copyfile(filemean,backupfile);%make backup
    2499             if ~isequal(success,1)
    2500                 msgbox_uvmat('ERROR',['previous file result ' filemean ' already exists, problem in backup'])
    2501                 return
    2502             end
    2503         end
    2504         if isequal(Atype{1},'uint16')
    2505             imwrite(uint16(DataMean.A),filemean,'BitDepth',16);
    2506         else
    2507             imwrite(uint8(DataMean.A),filemean,'BitDepth',8);
    2508         end
    2509         display([filemean ' written']);
    2510     else %determine global attributes
    2511         DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {Series.Action}];
    2512         ActionKey='Action';
    2513         while isfield(DataMean,ActionKey)
    2514             ActionKey=[ActionKey '_1'];
    2515         end
    2516         eval(['DataMean.' ActionKey '=Series.Action;'])
    2517         DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {ActionKey}];
    2518         if isfield(DataMean,'Time')
    2519             DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {'Time','Time_end'}];
    2520         end 
    2521         if NbSlice==1
    2522           filemean=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.nc',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end));
    2523         else % label the file number by the slice # for simplicity
    2524           [filemean]=name_generator(filebase_out,i_slice,1,'.nc','_i');
    2525         end
    2526         if exist(filemean,'file')
    2527             backupfile=filemean;
    2528             testexist=2;
    2529             while testexist==2
    2530                 backupfile=[backupfile(1:end-3) '~.nc'];
    2531                 testexist=exist(backupfile,'file');
    2532             end
    2533             [success,message]=copyfile(filemean,backupfile);%make backup
    2534             if ~isequal(success,1)
    2535                 msgbox_uvmat('ERROR',['previous file result ' filemean ' already exists, problem in backup'])
    2536                 display(['previous file result ' filemean ' already exists, problem in backup'])
    2537                 return
    2538             end
    2539         end
    2540         errormsg=struct2nc(filemean,DataMean); %save result file
    2541         if isempty(errormsg)
    2542             display([filemean ' written']);
    2543         else
    2544             msgbox_uvmat('ERROR',['error in writting result file: ' errormsg])
    2545             display(errormsg)
    2546         end
    2547    end
    2548 end
    2549 hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
    2550 delete(hget_field)
    2551 'TEST'
    2552 uvmat(filemean)
    2553 
    2554 
    25551921% %----------------------------------------------------------------------
    25561922% % --makes a time averaged velocity field
     
    33372703   
    33382704   
    3339 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    3340  %detect the chosen series of files and check their date of modification:
    3341 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    3342 %INPUT:
    3343 %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    3344 %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    3345 %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
    3346 %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
    3347 %OTHER INPUTS given by the structure Series
    3348 function GUI_input=clean_civ_cmx(num_i1,num_i2,num_j1,num_j2,Series) %(filecell,filecell_1,num_i,num_j,vel_type,field,param);
    3349 
    3350 %requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
    3351 if ~exist('num_i1','var')
    3352     GUI_input={'RootPath';'many';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
    3353         'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
    3354         %'RootFile';'on';... %root input file name ('on' by default)
    3355         %'FileExt';'on';... %input file extension ('on' by default)
    3356         %'NomType';'on';...%type of file indexing ('on' by default)
    3357         %'NbSlice';'on'; ...%nbre of slices ('off' by default)
    3358         %'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default)
    3359         %'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
    3360         %'CoordType';'on'...%can use a transform function 'off' by default
    3361         %'GetObject';'on'...%can use projection object ,'off' by default
    3362         %'GetMask';'on'...%can use mask option   ,'off' by default
    3363         %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter
    3364                ''};
    3365     return %exit the function
    3366 end
    3367 %---------------------------------------------------------
    3368 hseries=guidata(Series.hseries);%handles of the GUI series
    3369 WaitbarPos=get(hseries.waitbar_frame,'Position');
    3370 
    3371 %%%%%%%%%%%%%%%%%%%%%%%%
    3372 message='this function will delete all files with extensions .log, .bat, .cmx,.cmx2,.errors in the input directory(ies)';
    3373 answer=msgbox_uvmat('INPUT_Y-N',message);
    3374 if ~isequal(answer,'Yes')
    3375     return
    3376 end
    3377 nbdelete=0;
    3378 testcell=iscell(Series.RootFile);
    3379 if ~testcell
    3380     Series.RootPath={Series.RootPath};
    3381     Series.RootFile={Series.RootFile};
    3382     Series.SubDir={Series.SubDir};
    3383     Series.FileExt={Series.FileExt};
    3384     Series.NomType={Series.NomType};
    3385 end
    3386 for iview=1:length(Series.RootFile)
    3387     hdir=dir(fullfile(Series.RootPath{iview},Series.SubDir{iview}));%list files
    3388     for ilist=1:length(hdir)
    3389         update_waitbar(hseries.waitbar,WaitbarPos,ilist/length(hdir))
    3390         FileName=hdir(ilist).name;
    3391         [dd,ff,Ext]=fileparts(FileName);
    3392         if isequal(Ext,'.log')||isequal(Ext,'.bat')||isequal(Ext,'.cmx')||isequal(Ext,'.cmx2')|| isequal(Ext,'.errors')
    3393             delete(fullfile(Series.RootPath{iview},Series.SubDir{iview},FileName))
    3394             nbdelete=nbdelete+1;
    3395         end
    3396     end
    3397 end
    3398 msgbox_uvmat('CONFIRMATION',['END: ' num2str(nbdelete) ' files deleted by clean_civ_cmx'])
    3399 
    3400 
    3401 
    34022705
    34032706
     
    36072910
    36082911
    3609 %----------------------------------------------------------------------
    3610 % --- make a time series analysis
    3611 %----------------------------------------------------------------------
    3612 %INPUT:
    3613 %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    3614 %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    3615 %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
    3616 %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
    3617 %OTHER INPUTS given by the structure Series
    3618 function GUI_input=time_series(num_i1,num_i2,num_j1,num_j2,Series)
    3619 
    3620 %requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
    3621 if ~exist('num_i1','var')
    3622     GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
    3623         'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
    3624         'RootFile';'on';... %root input file name ('on' by default)
    3625         'FileExt';'on';... %input file extension ('on' by default)
    3626         'NomType';'on';...%type of file indexing ('on' by default)
    3627         'NbSlice';'on'; ...%nbre of slices ('off' by default)
    3628         'VelTypeMenu';'two';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default)
    3629         'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
    3630         'CoordType';'on';...%can use a transform function 'off' by default
    3631         'GetObject';'on';...%can use projection object ,'off' by default
    3632         %'GetMask';'on'...%can use mask option   ,'off' by default
    3633         %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter
    3634                ''};
    3635     return %exit the function
    3636 end
    3637 
    3638 %------------------------------------------------------
    3639 hseries=guidata(Series.hseries);%handles in the GUI series
    3640 WaitbarPos=get(hseries.waitbar_frame,'Position'); %position of the waitbar frame
    3641 
    3642 %projection object
    3643 test_object=get(hseries.GetObject,'Value');
    3644 if test_object%isfield(Series,'sethandles')
    3645     Series.ProjObject=read_set_object(Series.sethandles);
    3646     %answeryes=questdlg({['field series projected on ' Series.ProjObject.Style]});
    3647     answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' Series.ProjObject.Style]);
    3648     if ~isequal(answeryes,'Yes')
    3649         return
    3650     end
    3651 else
    3652     msgbox_uvmat('ERROR','a projection object is needed');
    3653     return
    3654 end
    3655 
    3656 % root names
    3657 if iscell(Series.RootPath)
    3658     RootPath=Series.RootPath;
    3659     RootFile=Series.RootFile;
    3660     SubDir=Series.SubDir;
    3661     FileExt=Series.FileExt;
    3662     NomType=Series.NomType;
    3663 else
    3664     RootPath={Series.RootPath};
    3665     RootFile={Series.RootFile};
    3666     SubDir={Series.SubDir};
    3667     FileExt={Series.FileExt};
    3668     NomType={Series.NomType};
    3669     num_i1={num_i1};
    3670     num_i2={num_i2};
    3671     num_j1={num_j1};
    3672     num_j2={num_j2};
    3673 end
    3674 ext=FileExt{1};
    3675 form=imformats(ext([2:end]));%test valid Matlab image formats
    3676 testima=0;
    3677 if ~isempty(form)||isequal(lower(ext),'.avi')
    3678     testima=1;
    3679 end
    3680 nbview=length(RootPath);%number of series (1 or 2)
    3681 nbfield=size(num_i1{1},1)*size(num_i1{1},2); %number of fields in the time series
    3682 
    3683 %Number of input series: this function  accepts only a single input file series
    3684 nbview=length(RootPath);
    3685 if nbview==2
    3686     %TODO: choose between difference and two series
    3687 elseif nbview>2  % TODO: make multiple series
    3688 %     RootPath=RootPath(1:2);
    3689 %     set(hseries.RootPath,'String',RootPath)
    3690 %     SubDir=SubDir(1:2);
    3691 %     set(hseries.SubDir,'String',SubDir)
    3692 %     RootFile=RootFile(1:2);
    3693 %     set(hseries.RootFile,'String',RootFile)
    3694 %     NomType=NomType(1:2);
    3695 %     %set(hseries.NomType,'String',NomType)
    3696 %     FileExt=FileExt(1:2);
    3697 %     set(hseries.FileExt,'String',FileExt)
    3698 %     nbview=2;
    3699 end
    3700 hhh=which('mmreader');
    3701 for iview=1:nbview
    3702     test_movie(iview)=0;
    3703     if ~isequal(hhh,'')&& mmreader.isPlatformSupported()
    3704         if isequal(lower(FileExt{iview}),'.avi')
    3705             MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}]));
    3706             test_movie(iview)=1;
    3707         end
    3708     end
    3709 end
    3710 filebase{1}=fullfile(RootPath{1},RootFile{1});
    3711 
    3712 % number of slices
    3713 NbSlice=str2num(get(hseries.NbSlice,'String'));
    3714 if isempty(NbSlice)
    3715     NbSlice=1;
    3716 end
    3717 NbSlice_name=num2str(NbSlice);
    3718 
    3719 % Field and velocity type (the same for the two views)
    3720 if isfield(Series,'Field')
    3721     FieldName=Series.Field;%the same set of fields for all views
    3722 else
    3723     FieldName={''};
    3724 end
    3725 if isequal(FieldName,{'get_field...'})
    3726     hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
    3727     if numel(hget_field)>1
    3728         delete(hget_field(2:end)) % delete multiple occurerence of the GUI get_fioeld
    3729     elseif isempty(hget_field)
    3730        filename=name_generator(filebase{1},num_i1{1}(1),num_j1{1}(1),FileExt{1},NomType{1},1,num_i2{1}(1),num_j2{1}(1),SubDir{1});
    3731        idetect(iview)=exist(filename,'file');
    3732        hget_field=get_field(filename);
    3733        return
    3734     end
    3735     %hhget_field=guidata(hget_field);%handles of GUI elements in get_field
    3736     SubField=read_get_field(hget_field) %read the names of the variables to plot in the get_field GUI
    3737     if isempty(SubField)
    3738         delete(hget_field)
    3739        filename=name_generator(filebase{1},num_i1{1}(1),num_j1{1}(1),FileExt{1},NomType{1},1,num_i2{1}(1),num_j2{1}(1),SubDir{1});
    3740         hget_field=get_field(filename);
    3741         SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
    3742     end
    3743 %     if isequal(get(hhget_field.menu_coord,'Visible'),'on')
    3744 %         list_transform=get(hhget_field.menu_coord,'String');
    3745 %         val_list=get(hhget_field.menu_coord,'Value');
    3746 %         transform=list_transform{val_list};
    3747 %     end
    3748 end
    3749 
    3750 %detect whether the two files are 'images' or 'netcdf'
    3751 testima=0;
    3752 testvol=0;
    3753 testcivx=0;
    3754 testnc=0;
    3755 FileExt=get(hseries.FileExt,'String');
    3756 for iview=1:nbview
    3757      ext=FileExt{iview};
    3758      form=imformats(ext([2:end]));
    3759      if isequal(lower(ext),'.vol')
    3760          testvol=testvol+1;
    3761      elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab
    3762          testima=testima+1;
    3763      elseif isequal(ext,'.nc')
    3764          testnc=testnc+1;
    3765      end
    3766 end
    3767 if testvol
    3768     msgbox_uvmat('ERROR','volume images not implemented yet')
    3769     return
    3770 end
    3771 if testnc~=nbview && testima~=nbview && testvol~=nbview
    3772     msgbox_uvmat('need a set of images or a set of netcdf files with the same fields as input','ERROR')
    3773     return
    3774 end
    3775 if ~isequal(FieldName,{'get_field...'})
    3776     testcivx=testnc;
    3777 end
    3778 
    3779 % Root name of output files (TO GENERALISE FOR TWO INPUT SERIES)
    3780 filebasesub=fullfile(RootPath{1},RootFile{1});
    3781 if NbSlice==1
    3782     filebase_out=[filebasesub '_time'];
    3783 else
    3784     filebase_out=[filebasesub '_' NbSlice_name 'mtim'];
    3785     increment=num_i1{1}(2)-num_i1{1}(1);
    3786     if ~isequal(increment,1) % if an increment is set
    3787         answeryes=msgbox_uvmat('INPUT_Y-N',['will take time series in ' num2str(NbSlice) 'slices with increment = ' num2str(increment) '!']);
    3788     else   
    3789         answeryes=msgbox_uvmat('INPUT_Y-N',{['will take time series in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_out ' ...']});
    3790     end
    3791     if ~isequal(answeryes,'Yes')
    3792         return
    3793     end
    3794 end
    3795 VelType_str=get(hseries.VelTypeMenu,'String');
    3796 VelType_val=get(hseries.VelTypeMenu,'Value');
    3797 VelType{1}=VelType_str{VelType_val};
    3798 if nbview==2
    3799     VelType_str=get(hseries.VelTypeMenu_1,'String');
    3800     VelType_val=get(hseries.VelTypeMenu_1,'Value');
    3801     VelType{2}=VelType_str{VelType_val};
    3802 end
    3803 
    3804 %Calibration data and timing: read the ImaDoc files
    3805 mode=''; %default
    3806 timecell={};
    3807 XmlData={};
    3808 itime=0;
    3809 NbSlice_calib={};
    3810 for iview=1:nbview%Loop on views
    3811     XmlData{iview}=[];%default
    3812     filebase{iview}=fullfile(RootPath{iview},RootFile{iview});
    3813     if exist([filebase{iview} '.xml'],'file')
    3814         [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']);
    3815         if isfield(XmlData{iview},'Time')
    3816             itime=itime+1;
    3817             timecell{itime}=XmlData{iview}.Time;
    3818         end
    3819         if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord')
    3820             NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
    3821             if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
    3822                 msgbox_uvmat('WARNING','inconsistent number of Z indices for the field series');
    3823             end
    3824         end
    3825     elseif exist([filebase{iview} '.civ'],'file')
    3826         [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']);
    3827         itime=itime+1;
    3828         timecell{itime}=time;
    3829         XmlData{iview}.Time=time;
    3830         GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
    3831         GeometryCalib.Tx=0;
    3832         GeometryCalib.Ty=0;
    3833         GeometryCalib.Tz=1;
    3834         GeometryCalib.dpx=1;
    3835         GeometryCalib.dpy=1;
    3836         GeometryCalib.sx=1;
    3837         GeometryCalib.Cx=0;
    3838         GeometryCalib.Cy=0;
    3839         GeometryCalib.f=1;
    3840         GeometryCalib.kappa1=0;
    3841         GeometryCalib.CoordUnit='cm';
    3842         XmlData{iview}.GeometryCalib=GeometryCalib;
    3843         if error==1
    3844             msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
    3845         end
    3846     end
    3847 end
    3848 
    3849 %check coincidence in time
    3850 multitime=0;
    3851 if length(timecell)==0
    3852     time=[];
    3853 elseif length(timecell)==1
    3854     time=timecell{1};
    3855 elseif length(timecell)>1
    3856     multitime=1;
    3857     for icell=1:length(timecell)
    3858         if ~isequal(size(timecell{icell}),size(timecell{1}))
    3859             warndlg_uvmat('inconsistent time array dimensions in ImaDoc fields, the time for the first series is used','WARNING')
    3860             time=timecell{1};
    3861             multitime=0;
    3862             break
    3863         end
    3864     end
    3865 end
    3866 if multitime
    3867     for icell=1:length(timecell)
    3868         time(icell,:,:)=timecell{icell};
    3869     end
    3870     diff_time=max(max(diff(time)));
    3871     if diff_time>0
    3872         warndlg_uvmat(['times of series differ by more than ' num2str(diff_time)],'WARNING')
    3873     end   
    3874 end
    3875 if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file'
    3876     time=[];
    3877 end
    3878 
    3879 % image or scalar processing programme set by user
    3880 Coord_menu=get(hseries.CoordType,'String');
    3881 menu_val=get(hseries.CoordType,'Value');
    3882 usrfct=Coord_menu{menu_val};
    3883 testfct=~isequal(usrfct,'');
    3884 
    3885 % to update:
    3886 VelType_str=get(hseries.VelTypeMenu,'String');
    3887 VelType_val=get(hseries.VelTypeMenu,'Value');
    3888 VelType{1}=VelType_str{VelType_val};
    3889 if nbview==2
    3890     VelType_str=get(hseries.VelTypeMenu_1,'String');
    3891     VelType_val=get(hseries.VelTypeMenu_1,'Value');
    3892     VelType{2}=VelType_str{VelType_val};
    3893 end
    3894 
    3895 %LOOP ON SLICES
    3896 for i_slice=1:NbSlice
    3897      dt=[];
    3898      nbmissing=0; %number of undetected files
    3899      nbfiles=0;
    3900     %%%%%%%%%%%%%%%%%%%%%%%%%%%%LOOP ON FIELDS IN  A SLICE
    3901     for ifile=i_slice:NbSlice:nbfield 
    3902         stopstate=get(hseries.RUN,'BusyAction');
    3903         if isequal(stopstate,'queue')% enable STOP command
    3904              update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield)
    3905              for iview=1:nbview
    3906                 filename=...
    3907                            name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),FileExt{iview},NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview});
    3908                 idetect(iview)=exist(filename,'file');
    3909                 Data{iview}=[]; %default     
    3910                 if testima                 
    3911                     Data{iview}.ListVarName={'A'};
    3912                     Data{iview}.AName='image';
    3913                     if test_movie(iview)
    3914                         A=read(MovieObject{iview},num_i1{iview}(ifile));
    3915                     else
    3916                         A=double(read_image(filename,NomType{iview},num_i1{iview}(ifile)));% read the image, num2 is the counter for avi files
    3917                     end
    3918                     Data{iview}.ListVarName={'coord_y','coord_x','A'}; %
    3919                     npy=size(A,1);
    3920                     npx=size(A,2);
    3921                     nbcolor=size(A,3);
    3922                     if nbcolor==3
    3923                          Data{iview}.VarDimName={'coord_y','coord_x',{'coord_y','coord_x','rgb'}};
    3924                     else
    3925                          Data{iview}.VarDimName={'coord_y','coord_x',{'coord_y','coord_x'}};
    3926                     end 
    3927                     Data{iview}.coord_y=[npy-0.5 0.5];
    3928                     Data{iview}.coord_x=[0.5 npx-0.5];
    3929                     Data{iview}.A=A;
    3930                     Data{iview}.CoordType='px';
    3931                 elseif testcivx
    3932                     [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType);
    3933                 else
    3934                     [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data               
    3935                     Data{iview}.VarAttribute=SubField.VarAttribute;
    3936                 end
    3937                 if ~isempty(NbSlice_calib)  % z index
    3938                     Data{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1;
    3939                 end
    3940              end
    3941             % geometry transform or other user defined transform
    3942             if ~isequal(Series.CoordType,'')           
    3943                 if nbview==2
    3944                     [Data{1},Data{2}]=feval(Series.CoordType,Data{1},XmlData{1},Data{2},XmlData{2});
    3945                     if isempty(Data{2})
    3946                         Data(2)=[];
    3947                     end
    3948                 else
    3949                     Data{1}=feval(Series.CoordType,Data{1},XmlData{1});
    3950                 end
    3951             end
    3952             if testcivx
    3953                     Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..)
    3954             end
    3955             if length(Data)==2
    3956                 [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields
    3957                 if ~isempty(errormsg)
    3958                     msgbox_uvmat('ERROR',['error in time_series/sub_field:' errormsg])
    3959                     return
    3960                 end
    3961             else
    3962                 Field=Data{1};
    3963             end
    3964             if isfield(Series,'ProjObject')
    3965                 Series.ProjObject
    3966                 [Field,errormsg]=proj_field(Field,Series.ProjObject);
    3967                 if ~isempty(errormsg)
    3968                     msgbox_uvmat('ERROR',['error in time_series/proj_field:' errormsg])
    3969                     return
    3970                 end
    3971             end
    3972             if min(idetect)>=1% the input file(s) have been detected         
    3973                 nbfiles=nbfiles+1;
    3974                 if nbfiles==1 %first field: initiate the time series
    3975                     RecordData=Field;%default
    3976                     RecordData.NbDim=Field.NbDim+1; %add the time dimension for plots         
    3977                     nbvar=length(Field.ListVarName);
    3978                     if nbvar==0
    3979                         msgbox_uvmat('ERROR','no input variable selected in get_field')
    3980                         return
    3981                     end
    3982                     testsum=2*ones(1,nbvar);%initiate flag for action on each variable
    3983                     indexfalse=0;
    3984                     CoordName={};
    3985                     indexremove=[];
    3986                     if isfield(Field,'VarAttribute') % look for coordinate and flag variables   
    3987                         for ivar=1:nbvar
    3988                             if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role')
    3989                                 var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable
    3990                                 if isequal(var_role,'errorflag')
    3991                                     msgbox_uvmat('ERROR','do not handle error flags in time series')
    3992                                     return                                               
    3993                                 end
    3994                                 if isequal(var_role,'warnflag')                       
    3995                                     testsum(ivar)=0;  % not recorded variable
    3996                                     eval(['RecordData=rmfield(RecordData,''' Field.ListVarName{ivar} ''');']);%remove variable
    3997                                 end                 
    3998                                 if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|...
    3999                                     isequal(var_role,'coord_z')|isequal(var_role,'coord')
    4000                                     testsum(ivar)=1; %constant coordinates, record without time evolution
    4001                                 end
    4002                                 % check whether the variable ivar is a dimension variable
    4003                                 %index=Field.VarDimIndex{ivar};%dimension indices of the variable #ivar
    4004                                 DimCell=Field.VarDimName{ivar};
    4005                                 if ischar(DimCell)
    4006                                     DimCell={DimCell};
    4007                                 end
    4008                                 if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables
    4009                                    testsum(ivar)=1;
    4010                                 end
    4011                             end
    4012                         end
    4013                     end
    4014                     for ivar=1:nbvar
    4015                         if testsum(ivar)==2                     
    4016                             eval(['RecordData.' Field.ListVarName{ivar} '=[];'])
    4017                         end
    4018                     end
    4019                     RecordData.ListVarName=[{'Time'} RecordData.ListVarName];
    4020                 end
    4021                 for ivar=1:length(Field.ListVarName)
    4022                     VarName=Field.ListVarName{ivar};
    4023                     eval(['VarVal=Field.' VarName ';']);
    4024                     if testsum(ivar)==2% test for recorded variable
    4025                         eval(['VarVal=Field.' VarName ';']);
    4026                         if isequal(Series.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode
    4027                             if isempty(VarVal)
    4028                                 msgbox_uvmat('ERROR',['empty result at frame index ' num2str(num_i1{iview}(ifile))])
    4029                                 return                             
    4030                             end
    4031                             VarVal=mean(VarVal,1);
    4032                         end
    4033                         VarVal=shiftdim(VarVal,-1); %shift dimension
    4034                         eval(['RecordData.' VarName '=cat(1,RecordData.' VarName ',VarVal);']);%concanete the current field to the time series   
    4035                     elseif testsum(ivar)==1% variable representing fixed coordinates
    4036                         eval(['VarInit=RecordData.' VarName ';']);
    4037                         if ~isequal(VarVal,VarInit)
    4038                             msgbox_uvmat('ERROR',['time series requires constant coordinates ' VarName])
    4039                             return
    4040                         end
    4041                     end                 
    4042                 end
    4043                 % time:
    4044                 if isempty(time)% time read in ncfiles
    4045                    if isfield(Field,'Time')
    4046                        RecordData.Time(nbfiles,1)=Field.Time;
    4047                    else
    4048                        RecordData.Time(nbfiles,1)=nbfiles;%default
    4049                    end
    4050                 else % time from ImaDoc prevails
    4051                     RecordData.Time(nbfiles,1)=(time(1,num_i1{1}(ifile),num_j1{1}(ifile))+time(end,num_i2{end}(ifile),num_j2{end}(ifile)))/2;
    4052                 end
    4053             else
    4054                 nbmissing=nbmissing+1;
    4055             end
    4056         end
    4057     end
    4058     %remove time for global attributes if exists
    4059     for iattr=1:numel(RecordData.ListGlobalAttribute)
    4060         if strcmp(RecordData.ListGlobalAttribute{iattr},'Time')
    4061             RecordData.ListGlobalAttribute(iattr)=[];
    4062             break
    4063         end
    4064     end
    4065     for ivar=1:numel(RecordData.ListVarName)
    4066         VarName=RecordData.ListVarName{ivar};
    4067         eval(['RecordData.' VarName '=squeeze(RecordData.' VarName ');']) %remove singletons
    4068     end
    4069         % add time dimension and update VarDimIndex:
    4070    %if ~isequal(Series.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode
    4071         for ivar=1:length(Field.ListVarName)
    4072 %              vardimindex=Field.VarDimIndex{ivar};% array of dimension indices for variable VarIndex(ivar)
    4073              DimCell=Field.VarDimName(ivar);
    4074              if testsum(ivar)==2%variable used as time series
    4075 %                  RecordData.VarDimIndex{ivar}=[1 vardimindex+1];
    4076                   RecordData.VarDimName{ivar}=[{'Time'} DimCell];
    4077              elseif testsum(ivar)==1
    4078 %                  RecordData.VarDimIndex{ivar}=[vardimindex+1];
    4079                  RecordData.VarDimName{ivar}=DimCell;
    4080              end
    4081         end
    4082    % end
    4083     indexremove=find(~testsum);
    4084     if ~isempty(indexremove)
    4085         RecordData.ListVarName(1+indexremove)=[];
    4086         RecordData.VarDimName(indexremove)=[];
    4087         if isfield(RecordData,'Role')&~isempty(RecordData.Role{1})%generaliser aus autres attributs
    4088             RecordData.Role(1+indexremove)=[];
    4089         end
    4090     end
    4091     %RecordData.VarDimIndex=[{[1]} RecordData.VarDimIndex]; %time dimension
    4092     %shift variable attributes
    4093     if isfield(RecordData,'VarAttribute')
    4094         RecordData.VarAttribute=[{[]} RecordData.VarAttribute];
    4095     end
    4096     RecordData.VarDimName=[{'Time'} RecordData.VarDimName];
    4097     RecordData.Action=Series.Action;%name of the processing programme
    4098     %name of result file
    4099     [filemean]=...
    4100                name_generator(filebase_out,num_i1{1}(i_slice),num_j1{1}(i_slice),'.nc','_i1-i2_j1-j2',1,num_i2{end}(ifile),num_j2{end}(ifile),SubDir{1});
    4101     errormsg=struct2nc(filemean,RecordData); %save result file
    4102     if isempty(errormsg)
    4103         display([filemean ' written'])
    4104     else
    4105         msgbox_uvmat('ERROR',['error in Series/struct2nc' errormsg])
    4106     end
    4107 end
    4108 figure
    4109 haxes=axes;
    4110 
    4111 plot_field(RecordData,haxes)
    4112 hget_field=findobj(allchild(0),'name','get_field');
    4113 if ~isempty(hget_field)
    4114     delete(hget_field)
    4115 end
    4116 get_field(filemean,RecordData)
    4117    
    4118 %-----------------------------------------------------------------------
    4119 % --- Executes on selection change in CoordType.
    4120 function CoordType_Callback(hObject, eventdata, handles)
    4121 menu_str=get(handles.CoordType,'String');
    4122 ind_coord=get(handles.CoordType,'Value');
    4123 coord_option=menu_str{ind_coord};
    4124 if isequal(coord_option,'more...');
    4125     fct_name='';
    4126     if exist('./TMP/current_usr_fct.mat','file')% if a file is found
    4127         h=load('./TMP/current_usr_fct.mat');
    4128         if isfield(h,'fct_name');
    4129             fct_name=h.fct_name;
    4130         end
    4131     end
    4132     prompt = {'Enter the name of the transform function'};
    4133     dlg_title = 'user defined transform';
    4134     num_lines= 1;
    4135     [FileName, PathName, filterindex] = uigetfile( ...
    4136        {'*.m', ' (*.m)';
    4137         '*.m',  '.m files '; ...
    4138         '*.*', 'All Files (*.*)'}, ...
    4139         'Pick a file', fct_name);
    4140     fct_name=fullfile(PathName,FileName);
    4141     addpath(PathName);%add the path to the selected fct
    4142     [errormsg,date_str]=check_functions;%check whether new functions can oversed the uvmat package A UTILISER
    4143     if ~exist(fct_name,'file')
    4144            warndlg(['image procesing fct ' fct_name ' not found'])
    4145     else
    4146         transform=FileName(1:end-2);%
    4147         update_menu(handles.CoordType,transform)%add the selected fct to the menu
    4148   %      set(handles.mouse_coord,'String',menu([1:end-1])')%update the mouse coord menu
    4149       %save ('./TMP/current_usr_fct.mat','fct_name');
    4150     end   
    4151 end
    4152 ind_coord=get(handles.CoordType,'Value');   
    4153 
    4154 %---------------------------------------------------------------------
    4155 % --- Executes on selection change in ProjObject.
    4156 function ProjObject_Callback(hObject, eventdata, handles)
    4157 
    4158 list_object=get(handles.ProjObject,'String');
    4159 index=get(handles.ProjObject,'Value');
    4160 hseries=get(handles.ProjObject,'Parent');
    4161 SeriesData=get(hseries,'UserData');
    4162 Obj=SeriesData.ProjObject{index};
    4163 [SeriesData.hset_object,SeriesData.sethandles]=set_object(SeriesData.ProjObject{index});
    4164 set(hseries,'UserData',SeriesData);
    4165 
    4166 %-------------------------------------------------------------
    4167 %generates a series of file names with reference numbers between range1 and
    4168 %range2 with increment incr. The reference number num_ref is the image number at the middle of the
    4169 %image pair. The set of first numbers num1 of the image pairs is also
    4170 %given as output
    4171 %------------------------------------------------------
    4172 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)
    4173 [Path,Name]=fileparts(filebase);
    4174 filebasesub=fullfile(Path,subdir,Name);
    4175 filecell={};%default
    4176 num_i1=[];
    4177 num_i2=[];
    4178 num_j1=[];
    4179 num_j2=[];
    4180 ind0_i=first_i:incr_i:last_i;
    4181 nbcolumn=length(ind0_i);
    4182 ind0_j=first_j:incr_j:last_j;
    4183 nbline=length(ind0_j);
    4184 if isequal(mode,'#_ab')
    4185     dirpair=dir([filebasesub '*_*.nc']);
    4186 elseif isequal(mode,'bursts')|isequal(mode,'series(Dj)') 
    4187     dirpair=dir([filebasesub '_*_*-*.nc']);
    4188 elseif isequal(mode,'series(Di)')
    4189     dirpair=dir([filebasesub '_*-*_*.nc']);
    4190 else
    4191     errordlg('option *|* not yet implemented')
    4192     return
    4193 end
    4194 if isempty(dirpair)
    4195         errordlg('no pair detected in the selected range')
    4196         return
    4197 end
    4198     %ind0_i=first_i:incr_i:last_i;
    4199     %nbcolumn=length(ind0_i);
    4200     %dirpair=dir([filebasesub '_*_*-*.nc']);
    4201 if isequal(mode,'bursts')|isequal(mode,'#_ab')
    4202     icount=0;
    4203     for ifile=1:length(dirpair)
    4204         [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
    4205        
    4206 %         if isempty(str2num(str_1))
    4207 %             dirpair(ifile).name
    4208 %         end
    4209         num1_r=str2num(str_1);
    4210         if isequal(RootFile,Name) & ~isempty(num1_r)   
    4211             num_i1(ifile)=num1_r;
    4212             num_a(ifile)=stra2num(str_a);
    4213             num_b(ifile)=stra2num(str_b);
    4214 %             icount=icount+1;
    4215         end     
    4216     end
    4217     length(dirpair)
    4218 %     num_j=floor((num_a+num_b)/2); %list of reference indices of the detected files
    4219     test_range= (num_i1 >=first_i)&(num_i1<= last_i);% =1 when both numbers are in the range
    4220     ind_i=((num_i1-first_i)/incr_i)+1;%indices i in the list of prescribed file indices
    4221     select=find(test_range &(floor(ind_i)==ind_i));%selected indices of num_i1 in the file directory
    4222     ind_i=ind_i(select);%set of selected indices ind_i
    4223     [ind_i,indsort]=sort(ind_i);%sorted list of ind_i
    4224     select=select(indsort);
    4225     num_i1=num_i1(select);
    4226     num_a=num_a(select);
    4227     num_b=num_b(select);
    4228     dirpair=dirpair(select);
    4229     [ind_remove]=find_pairs(dirpair,ind_i,nbcolumn);
    4230     ind_i(ind_remove)=[];
    4231     num_a(ind_remove)=[];
    4232     num_b(ind_remove)=[];
    4233     num_j1=zeros(1,nbcolumn);%default
    4234     num_j2=num_j1;
    4235     num_j1(ind_i)=num_a;
    4236     num_j2(ind_i)=num_b;
    4237     num_i1=first_i:incr_i:last_i;
    4238     num_i2=num_i1;
    4239     nbmissing=nbcolumn-length(ind_i);
    4240 
    4241 elseif isequal(mode,'series(Di)')
    4242     %ind0_i=first_i:incr_i:last_i;
    4243     %nbcolumn=length(ind0_i);
    4244     %ind0_j=first_j:incr_j:last_j;
    4245     %nbline=length(ind0_j);
    4246     %dirpair=dir([filebasesub '_*-*_*.nc']);
    4247     for ifile=1:length(dirpair)
    4248         [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
    4249         num_i1_r(ifile)=str2num(str_1);
    4250         num_i2_r(ifile)=str2num(str_2);
    4251         num_j(ifile)=str2num(str_a);
    4252     end
    4253     num_i=floor((num_i1_r+num_i2_r)/2); %list of reference indices of the detected files
    4254     test_range= (num_i >=first_i)&(num_i<= last_i)&(num_j >=first_j)&(num_j<= last_j);% =1 when both numbers are in the range
    4255     ind_i=((num_i-first_i)/incr_i)+1;%indices i and j in the list of prescribed file indices
    4256     ind_j=((num_j-first_j)/incr_j)+1;
    4257     ind_ij=ind_j+nbline*(ind_i-1);%indices in the reshhaped series of prescribed file indices
    4258     select=find(test_range &(floor(ind_i)==ind_i)&(floor(ind_j)==ind_j));%selected indices in the file directory
    4259     ind_ij=ind_ij(select);%set of selected indices ind_ij
    4260     [ind_ij,indsort]=sort(ind_ij);%sorted list of ind_ij
    4261     select=select(indsort);
    4262     num_i1_r=num_i1_r(select);
    4263     num_i2_r=num_i2_r(select);
    4264 %     num_j=num_j(select);
    4265     dirpair=dirpair(select);
    4266     [ind_remove]=find_pairs(dirpair,ind_ij,nbcolumn*nbline) ;
    4267     ind_ij(ind_remove)=[];
    4268     num_i1_r(ind_remove)=[];
    4269     num_i2_r(ind_remove)=[];
    4270     num_i1=zeros(1,nbline*nbcolumn);%default
    4271     num_i2=num_i1;
    4272     num_i1(ind_ij)=num_i1_r;
    4273     num_j2(ind_ij)=num_i2_r;
    4274     num_i1=reshape(num_i1,nbline,nbcolumn);
    4275     num_i2=reshape(num_i2,nbline,nbcolumn);
    4276     num_j1=meshgrid(ind0_i,ind0_j);
    4277     num_j2=num_j1;
    4278     nbmissing=nbline*nbcolumn-length(ind_ij);
    4279 elseif isequal(mode,'series(Dj)')
    4280  %   ind0_i=first_i:incr_i:last_i;
    4281  %   nbcolumn=length(ind0_i);
    4282  %   ind0_j=first_j:incr_j:last_j;
    4283   %  nbline=length(ind0_j);
    4284   %  dirpair=dir([filebasesub '_*_*-*.nc']);
    4285     for ifile=1:length(dirpair)
    4286         [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
    4287         num_i(ifile)=str2num(str_1);
    4288         num_a(ifile)=str2num(str_a);
    4289         num_b(ifile)=str2num(str_b);
    4290     end
    4291     num_j=floor((num_a+num_b)/2); %list of reference indices of the detected files
    4292     test_range= (num_i >=first_i)&(num_i<= last_i)&(num_j >=first_j)&(num_j<= last_j);% =1 when both numbers are in the range
    4293     ind_i=((num_i-first_i)/incr_i)+1;%indices i and j in the list of prescribed file indices
    4294     ind_j=((num_j-first_j)/incr_j)+1;
    4295     ind_ij=ind_j+nbline*(ind_i-1);%indices in the reshhaped series of prescribed file indices
    4296     select=find(test_range &(floor(ind_i)==ind_i)&(floor(ind_j)==ind_j));%selected indices in the file directory
    4297     ind_ij=ind_ij(select);%set of selected indices ind_ij
    4298     [ind_ij,indsort]=sort(ind_ij);%sorted list of ind_ij
    4299     select=select(indsort);
    4300     num_i=num_i(select);
    4301     num_a=num_a(select);
    4302     num_b=num_b(select);
    4303     dirpair=dirpair(select);
    4304     [ind_remove]=find_pairs(dirpair,ind_ij,nbcolumn*nbline) ;
    4305     ind_ij(ind_remove)=[];
    4306     num_a(ind_remove)=[];
    4307     num_b(ind_remove)=[];
    4308     num_j1=zeros(1,nbline*nbcolumn);%default
    4309     num_j2=num_j1;
    4310     num_j1(ind_ij)=num_a;
    4311     num_j2(ind_ij)=num_b;
    4312     num_j1=reshape(num_j1,nbline,nbcolumn);
    4313     num_j2=reshape(num_j2,nbline,nbcolumn);
    4314     num_i1=meshgrid(ind0_i,ind0_j);
    4315     num_i2=num_i1;
    4316     nbmissing=nbline*nbcolumn-length(ind_ij);
    4317 %     for i=1:length(indsel);%A SUPPRIMER ULTERIEUREMENT
    4318 %         if indsel(i)==0
    4319 %             filecell{i}='';
    4320 %         else
    4321 %             Name=dirpair(indsel(i)).name;
    4322 %             filecell{i}=fullfile(Path,subdir,Name);
    4323 %         end
    4324 %     end
    4325 %else
    4326 %    errordlg('option *|* not yet implemented')
    4327 %    return
    4328 end
     2912
    43292913
    43302914%%%%%%%%%%%%%
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