Changeset 774


Ignore:
Timestamp:
May 10, 2014, 12:50:36 AM (11 years ago)
Author:
sommeria
Message:

bug corrected in sub_background. test_patch1 introduced in civ_series

Location:
trunk/src/series
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/series/civ_input.m

    r771 r774  
    5656guidata(hObject, handles); % Update handles structure
    5757set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display)
    58 hseries=findobj(allchild(0),'Tag','series');
    59 hhseries=guidata(hseries);
    60 %SeriesData.ParentHandle=hseries;
    61 SeriesData=get(hseries,'UserData');
    62 % relevant data in gcbf:.FileType,.FileInfo,.Time,.TimeUnit,.GeometryCalib{1};
     58set(hObject,'WindowKeyPressFcn',{@keyboard_callback,handles})%set keyboard action function
     59set(handles.ref_i,'KeyPressFcn',{@ref_i_KeyPressFcn,handles})%set keyboard action function
     60%set(hObject,'WindowKeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
     61hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
     62hhseries=guidata(hseries); %handles of the elements in 'series'
     63SeriesData=get(hseries,'UserData');% info stored in the GUI series
    6364
    6465%% set visibility options:
    6566if strcmp(Param.Action.ActionName,'civ_series')
    66         set(handles.Program,'String','civ_series')
    67         set(handles.num_MaxDiff,'Visible','on')
    68         set(handles.num_MaxVel,'Visible','on')
    69         set(handles.title_MaxVel,'Visible','on')
    70         set(handles.title_MaxDiff,'Visible','on')
    71         set(handles.num_Nx,'Visible','off')
    72         set(handles.num_Ny,'Visible','off')
    73         set(handles.title_Nx,'Visible','off')
    74         set(handles.title_Ny,'Visible','off')
    75         set(handles.num_CorrSmooth,'Style','popupmenu')
    76         set(handles.num_CorrSmooth,'Value',1)
    77         set(handles.num_CorrSmooth,'String',{'1';'2'})
    78         set(handles.CheckThreshold,'Visible','on')
    79         set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
    80         set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
     67    %  set(handles.Program,'String','civ_series')
     68    set(handles.num_MaxDiff,'Visible','on')
     69    set(handles.num_MaxVel,'Visible','on')
     70    set(handles.title_MaxVel,'Visible','on')
     71    set(handles.title_MaxDiff,'Visible','on')
     72    set(handles.num_Nx,'Visible','off')
     73    set(handles.num_Ny,'Visible','off')
     74    set(handles.title_Nx,'Visible','off')
     75    set(handles.title_Ny,'Visible','off')
     76    set(handles.num_CorrSmooth,'Style','popupmenu')
     77    set(handles.num_CorrSmooth,'Value',1)
     78    set(handles.num_CorrSmooth,'String',{'1';'2'})
     79    set(handles.CheckThreshold,'Visible','on')
     80    set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
     81    set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
    8182end
    8283
    8384%% input file info
    84 % RootPath=Param.InputTable{1,1};
    85 % %set(handles.RootPath,'String',RootPath)
    86 % RootFile=Param.InputTable{1,3};
    87 % SubDir=Param.InputTable{1,2};
    8885NomTypeInput=Param.InputTable{1,4};
    89 % FileExt=Param.InputTable{1,5};
    9086FileType='image';%fdefault
    9187FileInfo=[];
    9288if isfield(SeriesData,'FileType')&&isfield(SeriesData,'FileInfo')
    9389    FileType=SeriesData.FileType{1};%type of the first input file series
    94     FileInfo=SeriesData.FileInfo{1};
    95 else
    96     set(hhseries.REFRESH,'BackgroundColor',[1 0 1])
    97 %     msgbox_uvmat('ERROR','please refresh the input file series')
    98 %     return
    99 end
    100 
    101 
    102 %% case of netcdf file as input, get the processing stage and look for corresponding images
    103 % imageinput=fileinput;%default
    104 % TODO: insert image input in the GUI series
     90    FileInfo=SeriesData.FileInfo{1};% info on the first input file series
     91else
     92    set(hhseries.REFRESH,'BackgroundColor',[1 0 1])% indicate that the file input in series needs to be refreshed
     93end
     94
     95%% case of netcdf file as input, read the processing stage and look for corresponding images
    10596ind_opening=0;%default
    10697NomTypeNc='';
    … …  
    118109        if isempty(regexp(NomTypeInput,'[ab|AB|-]', 'once'))
    119110            set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
    120 %             set(handles.RootFile_1,'Visible','On');
    121111        else
    122112            set(handles.ListCompareMode,'Value',1)
    123113        end
    124         imageinput='';
    125         FileInput=SeriesData.RefFile{1};
    126         Data=nc2struct(FileInput,'ListGlobalAttribute','Civ2_ImageA','Civ1_ImageA','Civ2_ImageB','Civ1_ImageB');
     114%         FileInput=SeriesData.RefFile{1};
     115        [Data,tild,tild,errormsg]=nc2struct(FileInfo.FileName,[]);
     116        if ~isempty(errormsg)
     117            msgbox_uvmat('ERROR',['error in netcdf input file: ' errormsg])
     118            return
     119        end
    127120        [PathCiv1_ImageA,Civ1_ImageA,FileExtA]=fileparts(Data.Civ1_ImageA);
    128121        [PathCiv1_ImageB,Civ1_ImageB,FileExtA]=fileparts(Data.Civ1_ImageB);
    129         if ~isempty(Data.Civ2_ImageA)
     122        if isfield(Data,'Civ2_ImageA')
    130123            [PathCiv2_ImageA,Civ2_ImageA,FileExtA]=fileparts(Data.Civ2_ImageA);
    131124            [PathCiv2_ImageB,Civ2_ImageB,FileExtA]=fileparts(Data.Civ2_ImageB);
    … …  
    133126        if size(Param.InputTable,1)==1
    134127            series('display_file_name',hhseries,Data.Civ1_ImageA,'append');%append the image series to the input list
    135         end
    136         if isfield(Data,'Txt')
    137             errormsg=Data.Txt;
    138             return
    139             %TODO: introduce the image in the input table of series
    140128        end
    141129        [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ1_ImageA);
    … …  
    153141    set(handles.PairIndices,'Visible','off')
    154142end
    155 
    156 %% TODO: get corresponding image in nc case
    157143
    158144%% reinitialise menus
    … …  
    166152%% prepare the GUI with input parameters
    167153set(handles.ListCompareMode,'Visible','on')
    168 
    169 %display the parameters stored on the GUI series
    170154set(handles.ref_i,'String',num2str(Param.IndexRange.first_i))
    171155if isfield(Param.IndexRange,'first_j')
    … …  
    173157end
    174158
    175 %% set the civ_input options depending on the input file content when a nc file has been opened
    176 ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
    177 checkbox=zeros(size(ListOptions));%default
    178 if ind_opening==0%case of image opening, start with Civ1
    179     for index=1:numel(ListOptions)
    180         checkbox(index)=get(handles.(ListOptions{index}),'Value');
    181     end
    182     index_max=find(checkbox, 1, 'last' );
    183     if isempty(index_max),index_max=1;end
    184     for index=1:index_max
    185         set(handles.(ListOptions{index}),'Value',1)% select all operations starting from CIV1
    186     end
    187 else
    188     for index = 1:min(ind_opening,5)
    189         set(handles.(ListOptions{index}),'value',0)
    190     end
    191     set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
    192     for index = ind_opening+2:6
    193         set(handles.(ListOptions{index}),'value',0)
    194     end
    195 end
    196 
    197 
    198159%%  set the menus of image pairs and default selection for civ_input   %%%%%%%%%%%%%%%%%%%
    199 MaxIndex_i=Param.IndexRange.MaxIndex_i(iview_image);
    200 MinIndex_i=Param.IndexRange.MinIndex_i(iview_image);
    201 MaxIndex_j=1;%default
    202 MinIndex_j=1;
    203 if isfield(Param.IndexRange,'MaxIndex_j')&&isfield(Param.IndexRange,'MinIndex_j')...
    204      && numel(Param.IndexRange.MaxIndex_j')>=iview_image &&numel(Param.IndexRange.MinIndex_j')>=iview_image 
    205 MaxIndex_j=Param.IndexRange.MaxIndex_j(iview_image);
    206 MinIndex_j=Param.IndexRange.MinIndex_j(iview_image);
    207 end
     160
     161%% display the min and max indices for the whole file series
     162if size(SeriesData.i1_series{iview_image},2)==2 && min(min(SeriesData.i1_series{iview_image}(:,1,:)))==0
     163    MinIndex_j=1;% index j set to 1 by default
     164    MaxIndex_j=1;
     165    MinIndex_i=find(SeriesData.i1_series{iview_image}(1,2,:), 1 )-1;% min ref index i detected in the series (corresponding to the first non-zero value of i1_series, except for zero index)
     166    MaxIndex_i=find(SeriesData.i1_series{iview_image}(1,2,:),1,'last' )-1;%max ref index i detected in the series (corresponding to the last non-zero value of i1_series)
     167else
     168    ref_i=squeeze(max(SeriesData.i1_series{iview_image}(1,:,:),[],2));% select ref_j index for each ref_i
     169    ref_j=squeeze(max(SeriesData.j1_series{iview_image}(1,:,:),[],3));% select ref_i index for each ref_j
     170     MinIndex_i=min(find(ref_i))-1;
     171     MaxIndex_i=max(find(ref_i))-1;
     172     MaxIndex_j=max(find(ref_j))-1;
     173     MinIndex_j=min(find(ref_j))-1;
     174end
     175% MaxIndex_i=Param.IndexRange.MaxIndex_i(iview_image);
     176% MinIndex_i=Param.IndexRange.MinIndex_i(iview_image);
     177% MaxIndex_j=1;%default
     178% MinIndex_j=1;
     179% if isfield(Param.IndexRange,'MaxIndex_j')&&isfield(Param.IndexRange,'MinIndex_j')...
     180%         && numel(Param.IndexRange.MaxIndex_j')>=iview_image &&numel(Param.IndexRange.MinIndex_j')>=iview_image
     181%     MaxIndex_j=Param.IndexRange.MaxIndex_j(iview_image);
     182%     MinIndex_j=Param.IndexRange.MinIndex_j(iview_image);
     183% end
    208184CivInputData.MaxIndex_i=MaxIndex_i;
    209185CivInputData.MaxIndex_j=MaxIndex_j;
    … …  
    274250set(handles.CoordUnit,'String',CoordUnit)
    275251set(handles.SearchRange,'UserData', pxcm_search);
    276 
    277 %% set the reference indices from the input file indices
    278 num_ref_i=str2num(get(handles.ref_i,'String'));
    279 num_ref_j=str2num(get(handles.ref_j,'String'));
    280 
    281 update_CivOptions(handles,ind_opening)
    282 
    283 %% list the possible index pairs, depending on the option set in ListPairMode
    284 ListPairMode_Callback([], [], handles)
    285 ListPairCiv1_Callback(hObject, eventdata, handles)
    286 
    287 %% introduce the stored parameters if relevant
     252% indicate the min and max indices i and j on the GUI
     253set(handles.MinIndex_i,'String',num2str(MinIndex_i))
     254set(handles.MaxIndex_i,'String',num2str(MaxIndex_i))
     255set(handles.MinIndex_j,'String',num2str(MinIndex_j))
     256set(handles.MaxIndex_j,'String',num2str(MaxIndex_j))
     257
     258%% introduce the stored Civ parameters  if available (from previous input or ImportConfig in series)
    288259if isfield(Param,'ActionInput')
    289260    fill_GUI(Param.ActionInput,hObject);%fill the GUI with the parameters retrieved from the input Param
    290261    hcheckgrid=findobj(handles.civ_input,'Tag','CheckGrid');
    291262    for ilist=1:numel(hcheckgrid)
    292         if get(hcheckgrid(ilist),'Value')
     263        if get(hcheckgrid(ilist),'Value')% if a grid is used, do not show Dx and Dy for an automatic grid
    293264            hparent=get(hcheckgrid(ilist),'parent');%handles of the parent panel
    294265            hchildren=get(hparent,'children');
    295             %handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel
    296266            handle_dx=findobj(hchildren,'tag','num_Dx');
    297267            handle_dy=findobj(hchildren,'tag','num_Dy');
    … …  
    305275    end
    306276end
    307 % indicate max and min indices updated from input file series (not stored in Param.ActionInput)
    308 set(handles.MaxIndex_i,'String',num2str(MaxIndex_i));
    309 set(handles.MinIndex_i,'String',num2str(MinIndex_i));
    310 set(handles.MaxIndex_j,'String',num2str(MaxIndex_i));
    311 set(handles.MinIndex_j,'String',num2str(MinIndex_i));
     277
     278%% set the civ_input options, depending on the input file content if a nc file has been opened
     279ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
     280checkbox=zeros(size(ListOptions));%default
     281if ind_opening==0  %case of image opening, start with Civ1
     282    for index=1:numel(ListOptions)
     283        checkbox(index)=get(handles.(ListOptions{index}),'Value');
     284    end
     285    index_max=find(checkbox, 1, 'last' );
     286    if isempty(index_max),index_max=1;end
     287    for index=1:index_max
     288        set(handles.(ListOptions{index}),'Value',1)% select all operations starting from CIV1
     289    end
     290else  %case of netcdf file opening, start with the stage read in the file
     291    for index = 1:min(ind_opening,5)
     292        set(handles.(ListOptions{index}),'value',0)     
     293        fill_civ_input(Data,handles); %fill civ_input with the parameters retrieved from an input Civ file
     294    end
     295    set(handles.ConfigSource,'String',FileInfo.FileName);
     296    set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
     297    for index = ind_opening+2:6
     298        set(handles.(ListOptions{index}),'value',0)
     299    end
     300end
     301
     302%% set the reference indices from the input file indices
     303update_CivOptions(handles,ind_opening)% fill the menu of possible pairs
     304
     305%% list the possible index pairs, depending on the option set in ListPairMode
     306ListPairMode_Callback([], [], handles)
     307ListPairCiv1_Callback(hObject, eventdata, handles)
    312308
    313309%% set the GUI to modal: wait for OK to close
    … …  
    316312uiwait(handles.civ_input);
    317313
    318 
    319 
    320 %Program_Callback([],[], handles)
    321314
    322315%------------------------------------------------------------------------
    … …  
    341334end
    342335
    343 
    344 
    345336% -----------------------------------------------------------------------
    346337% -----------------------------------------------------------------------
    … …  
    348339function MenuHelp_Callback(hObject, eventdata, handles)
    349340% -----------------------------------------------------------------------
    350 path_civ=fileparts(which ('civ'));
    351 helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
    352 if isempty(dir(helpfile))
    353     msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
    354 else
    355     addpath (fullfile(path_civ,'uvmat_doc'))
    356     web([helpfile '#civ'])
    357 end
    358 
    359 
    360 %------------------------------------------------------------------------
    361 % --- general function activated for an input file series
    362 function errormsg=display_file_name(handles,fileinput)
    363 %------------------------------------------------------------------------
    364 
    365 %% scan the image file series
    366 [FilePath,FileName,ImaExt]=fileparts(imageinput);
    367 % detect the file type, get the movie object if relevant, and look for the corresponding file series:
    368 % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
    369 switch Param.FileType{1}
    370     case {'image','multimage','video','mmreader'}
    371     otherwise
    372         errormsg='invalid input file: enter an image, a movie or civ .nc file';
    373         return
    374 end
    375 set(handles.RootPath,'String',RootPath)
    376 set(handles.Civ1_ImageA,'String',SubDirImages)
    377 set(handles.Civ2_ImageB,'String',RootFile)
    378 if strcmp(ExtInput,'.nc')
    379     SubDirCiv=regexprep(SubDir,['^' SubDirImages],'');%suppress the root  SuddirImages;
    380 else
    381     SubDirCiv= '.civ';
    382 end
    383 set(handles.Civ1_ImageB,'String',SubDirCiv)
    384 set(handles.Civ2_ImageA,'String',SubDirCiv)
    385 browse=get(handles.RootPath,'UserData');
    386 browse.incr_pair=[0 0];%default
    387 
    388 %% scan the images if a civ_input file has been opened
    389 MinIndex_i=min(i1_series(i1_series>0));
    390 MinIndex_j=min(j1_series(j1_series>0));
    391 MaxIndex_i=max(i1_series(i1_series>0));
    392 MaxIndex_j=max(j1_series(j1_series>0));
    393 
    394 %% look for an image documentation file
    395 XmlFileName=find_imadoc(RootPath,SubDir,RootFile,ImaExt);
    396 if isempty(XmlFileName)
    397     if (strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
    398         ext_imadoc=ImaExt;% the timing from the video movie is used
    399     else
    400         ext_imadoc='';
    401     end
    402 else
    403     [tild,tild,ext_imadoc]=fileparts(XmlFileName);
    404 end
    405 set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
    406 
    407 
    408 
    409 %% update i and j index range if a nc file has been opened or pb withmin max image indices:
    410 % then set first and last to the inputfile index by default
    411 first_i=str2num(get(handles.MinIndex_i,'String'));
    412 last_i=str2num(get(handles.last_i,'String'));
    413 if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i)||ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i
    414     first_i=num_ref_i;
    415     last_i=num_ref_i;
    416     set(handles.MinIndex_i,'String',num2str(first_i));
    417     set(handles.last_i,'String',num2str(last_i));%
    418 end
    419 
    420 %j index range
    421 first_j=str2num(get(handles.MinIndex_j,'String'));
    422 last_j=str2num(get(handles.last_j,'String'));
    423 if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)||ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j
    424     first_j=num_ref_j;
    425     last_j=num_ref_j;
    426     set(handles.MinIndex_j,'String',num2str(first_j));
    427     set(handles.last_j,'String',num2str(last_j));%
    428 end
    429 if num_ref_i>last_i || num_ref_i<first_i
    430     num_ref_i=round((first_i+last_i)/2);
    431 end
    432 if num_ref_j>last_j || num_ref_j<first_j
    433     num_ref_j=round((first_j+last_j)/2);
    434 end
    435 set(handles.ref_i,'String',num2str(num_ref_i))
    436 set(handles.ref_j,'String',num2str(num_ref_j))
    437 
    438 
    439 
    440 %% scan files to update the subdirectory list display
    441 listot=dir(RootPath);%directory of RootPath
    442 idir=0;
    443 listdir={''};%default
    444 % get the list of existing civ_input subdirectories in the path of theinput root  file
    445 for ilist=1:length(listot)
    446     if listot(ilist).isdir
    447         name=listot(ilist).name;
    448         if ~isequal(name,'.') && ~isequal(name,'..')
    449             idir=idir+1;
    450             listdir{idir,1}=listot(ilist).name;
    451         end
    452     end
    453 end
    454 
    455 %% store info
    456 %set(handles.RootPath,'UserData',browse)% store the nomenclature type
    457 
    458 %% list the possible index pairs, depending on the option set in ListPairMode
    459 ListPairMode_Callback([], [], handles)
     341web('http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#Civ')
    460342
    461343%------------------------------------------------------------------------
    … …  
    476358%     set(handles.ListSubdirCiv2,'Value',ilist)
    477359else % if Civ1 data already exist
    478     errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory
     360    errormsg=find_netcpair_civ(handles,1); %update the list of available index pairs in the new directory
    479361    if ~isempty(errormsg)
    480362    msgbox_uvmat('ERROR',errormsg)
    … …  
    550432checkbox(5)=get(handles.CheckFix2,'Value');
    551433checkbox(6)=get(handles.CheckPatch2,'Value');
    552 ind_selected=find(checkbox,1);
    553 set(handles.PairIndices,'Visible','on')
     434% ind_selected=find(checkbox,1);
     435set(handles.PairIndices,'Visible','on')% make the frame PaiIndices visible, choice of the index pairs fo civ
    554436if opening==0
    555437    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
    … …  
    715597        set(handles.ListPairMode,'String',{'series(Di)'})
    716598        ListPairMode_Callback(hObject, eventdata, handles)
    717         %         set(handles.RootFile_1,'Visible','Off');
    718         %         set(handles.sub_txt,'Visible','off')
    719         %         set(handles.RootFile_1,'String',[]);
    720         %         mode_store=get(handles.ListCompareMode,'UserData');
    721         %         set(handles.ListPairMode,'Visible','on')
    722         %         set(handles.ListPairMode,'Value',1)
    723         %         set(handles.ListPairMode,'String',{'series(Di)'})
    724         %         set(handles.CheckStereo,'Value',0)
    725         %         set(handles.last_j,'String',get(handles.MaxIndex_j,'String'))% select the whole volume scan by default
    726         %         set(handles.incr_i,'String',num2str(2))%
    727599    case 'displacement'
    728600        OriginIndex='on';%define a frame origin for displacement
    … …  
    1014886nbpair=200;%default
    1015887select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
    1016 testpair=0;
    1017888nbpair=200; %default
    1018889
    1019890%% determine the menu display in .ListPairCiv1
    1020 testpair=0; %TODO: check
    1021 if isequal(mode,'series(Di)')
    1022     if testpair
    1023         displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
    1024     else
     891switch mode
     892    case 'series(Di)'
    1025893        for ipair=1:nbpair
    1026894            if select(ipair)
    1027895                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
    1028                if ~checkframe
    1029                    if size(Time,1)>=ref_i+1+ceil(ipair/2) && size(Time,2)>=ref_j+1&& ref_i-floor(ipair/2)>=0 && ref_j>=0
    1030                  dt=Time(ref_i+1+ceil(ipair/2),ref_j+1)-Time(ref_i+1-floor(ipair/2),ref_j+1);%Time interval dtref_j+1
    1031                  displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
    1032                    end
     896                if ~checkframe
     897                    if size(Time,1)>=ref_i+1+ceil(ipair/2) && size(Time,2)>=ref_j+1&& ref_i-floor(ipair/2)>=0 && ref_j>=0
     898                        dt=Time(ref_i+1+ceil(ipair/2),ref_j+1)-Time(ref_i+1-floor(ipair/2),ref_j+1);%Time interval dtref_j+1
     899                        displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
     900                    end
    1033901                else
    1034902                    dt=ipair/1000;
    1035                       displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(ipair)];
    1036                end             
     903                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(ipair)];
     904                end
    1037905            else
    1038906                displ_pair{ipair}='...'; %pair not displayed in the menu
    1039907            end
    1040908        end
    1041     end
    1042 elseif isequal(mode,'series(Dj)')
    1043     if testpair
    1044         displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
    1045     else
     909    case 'series(Dj)'
    1046910        for ipair=1:nbpair
    1047911            if select(ipair)
    1048912                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
    1049                if ~checkframe
    1050                    if size(Time,2)>=ref_j+1+ceil(ipair/2) && size(Time,1)>=ref_i+1 && ref_j-floor(ipair/2)>=0 && ref_i>=0
    1051                  dt=Time(ref_i+1,ref_j+1+ceil(ipair/2))-Time(ref_i+1,ref_j+1-floor(ipair/2));%Time interval dtref_j+1
    1052                   displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
    1053                    end
     913                if ~checkframe
     914                    if size(Time,2)>=ref_j+1+ceil(ipair/2) && size(Time,1)>=ref_i+1 && ref_j-floor(ipair/2)>=0 && ref_i>=0
     915                        dt=Time(ref_i+1,ref_j+1+ceil(ipair/2))-Time(ref_i+1,ref_j+1-floor(ipair/2));%Time interval dtref_j+1
     916                        displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
     917                    end
    1054918                else
    1055919                    dt=ipair/1000;
    1056920                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
    1057                end                 
     921                end
    1058922            else
    1059923                displ_pair{ipair}='...'; %pair not displayed in the menu
    1060924            end
    1061925        end
    1062     end
    1063 elseif isequal(mode,'pair j1-j2')%case of pairs
    1064     MinIndex_j=CivInputData.MinIndex_j;
    1065     MaxIndex_j=min(CivInputData.MaxIndex_j,10);%limitate the number of pairs to 10x10
    1066     index_pair=0;
    1067     %get all the Time intervals in bursts   
    1068    for numod_a=MinIndex_j:MaxIndex_j-1 %nbfield2 always >=2 for 'pair j1-j2' mode
    1069         for numod_b=(numod_a+1):MaxIndex_j
    1070             index_pair=index_pair+1;
    1071             displ_pair{index_pair}=['j= ' num2stra(numod_a,nom_type_ima) '-' num2stra(numod_b,nom_type_ima)];
    1072             dt(index_pair)=numod_b-numod_a;%default dt
    1073             if size(Time,1)>ref_i && size(Time,2)>numod_b  % && ~checkframe
    1074                 dt(index_pair)=Time(ref_i+1,numod_b+1)-Time(ref_i+1,numod_a+1);% Time interval dt
    1075                  displ_pair{index_pair}=[displ_pair{index_pair} ' :dt= ' num2str(dt(index_pair)*1000)];
     926    case 'pair j1-j2'%case of pairs
     927        MinIndex_j=CivInputData.MinIndex_j;
     928        MaxIndex_j=min(CivInputData.MaxIndex_j,10);%limitate the number of pairs to 10x10
     929        index_pair=0;
     930        %get all the Time intervals in bursts
     931        for numod_a=MinIndex_j:MaxIndex_j-1 %nbfield2 always >=2 for 'pair j1-j2' mode
     932            for numod_b=(numod_a+1):MaxIndex_j
     933                index_pair=index_pair+1;
     934                displ_pair{index_pair}=['j= ' num2stra(numod_a,nom_type_ima) '-' num2stra(numod_b,nom_type_ima)];
     935                dt(index_pair)=numod_b-numod_a;%default dt
     936                if size(Time,1)>ref_i && size(Time,2)>numod_b  % && ~checkframe
     937                    dt(index_pair)=Time(ref_i+1,numod_b+1)-Time(ref_i+1,numod_a+1);% Time interval dt
     938                    displ_pair{index_pair}=[displ_pair{index_pair} ' :dt= ' num2str(dt(index_pair)*1000)];
     939                end
    1076940            end
    1077         end
    1078        
    1079     end
    1080     [dtsort,indsort]=sort(dt);
    1081     displ_pair=displ_pair(indsort);
    1082 elseif isequal(mode,'displacement')
    1083     displ_pair={'Di=Dj=0'};
     941           
     942        end
     943        [tild,indsort]=sort(dt);
     944        displ_pair=displ_pair(indsort);
     945    case 'displacement'
     946        displ_pair={'Di=Dj=0'};
    1084947end
    1085948if index==1
    1086 set(handles.ListPairCiv1,'String',displ_pair');
     949    set(handles.ListPairCiv1,'String',displ_pair');
    1087950end
    1088951
    … …  
    18231686% end
    18241687
     1688
     1689
     1690%------------------------------------------------------------------------
     1691%----function introduced for the correlation window figure, activated by deleting this window
     1692function closeview_field(gcbo,eventdata)
     1693%------------------------------------------------------------------------
     1694hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
     1695if ~isempty(hview_field)
     1696    delete(hview_field)
     1697end
     1698
     1699%------------------------------------------------------------------------
     1700% --- Executes on button press in CheckThreshold.
     1701function CheckThreshold_Callback(hObject, eventdata, handles)
     1702%------------------------------------------------------------------------
     1703huipanel=get(hObject,'parent');
     1704obj(1)=findobj(huipanel,'Tag','num_MinIma');
     1705obj(2)=findobj(huipanel,'Tag','num_MaxIma');
     1706obj(3)=findobj(huipanel,'Tag','title_Threshold');
     1707if get(hObject,'Value')
     1708    set(obj,'Visible','on')
     1709else
     1710    set(obj,'Visible','off')
     1711end
     1712
     1713%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     1714%%%%%%%%%%%%%%   TEST functions
     1715%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    18251716%------------------------------------------------------------------------
    18261717% --- Executes on button press in TestCiv1: prepare the image correlation function
    1827 % activated by mouse motion
     1718%     activated by mouse motion
    18281719function TestCiv1_Callback(hObject, eventdata, handles)
    18291720%------------------------------------------------------------------------
    … …  
    18311722if get(handles.TestCiv1,'Value')
    18321723    set(handles.TestCiv1,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch
    1833     ref_i=str2double(get(handles.ref_i,'String'));% read reference i index
    1834     if strcmp(get(handles.ref_j,'Visible'),'on')
    1835         ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant
    1836     else
    1837         ref_j=1;%default j index
    1838     end
    1839     % [filecell,i1,i2]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices
    1840     Data.ListVarName={'ny','nx','A'};
    1841     Data.VarDimName= {'ny','nx',{'ny','nx'}};
    1842     hseries=findobj(allchild(0),'Tag','series');
    1843     hhseries=guidata(hseries);
    1844     InputTable=get(hhseries.InputTable,'Data');
    1845     ind_A=1;
    1846     if strcmp(InputTable{1,5},'.nc');
    1847         ind_A=2;
    1848     end
    1849     list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
    1850     PairString=list_pair{get(handles.ListPairCiv1,'Value')};
    1851     [ind1,ind2,mode]=find_pair_indices(PairString,ref_i,ref_j);%,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
    1852     switch mode
    1853         case 'Di'
    1854             i1=ref_i-ind1;
    1855             i2=ref_i+ind2;
    1856             j1=ref_j;
    1857             j2=ref_j;
    1858         case 'Dj'
    1859             i1=ref_i;
    1860             i2=ref_i;
    1861             j1=ref_j-ind1;
    1862             j2=ref_j+ind2;
    1863         case 'burst'           
    1864             i1=ref_i;
    1865             i2=ref_i;
    1866             j1=ind1;
    1867             j2=ind2;
    1868     end
    1869     ImageName_A=fullfile_uvmat(InputTable{ind_A,1},InputTable{ind_A,2},InputTable{ind_A,3},InputTable{ind_A,5},InputTable{ind_A,4},...
    1870         i1,[],j1);
    1871         ImageName_B=fullfile_uvmat(InputTable{ind_A,1},InputTable{ind_A,2},InputTable{ind_A,3},InputTable{ind_A,5},InputTable{ind_A,4},...
    1872         i2,[],j2);
    1873     Data.A=imread(ImageName_A); % read the first image
    1874     if ndims(Data.A)==3 %case of color image
    1875         Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
    1876     end
    1877     Data.ny=[size(Data.A,1) 1];
    1878     Data.nx=[1 size(Data.A,2)];
    1879     Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly
    1880     par_civ1=read_GUI(handles.Civ1);
    1881     par_civ1.FileTypeA=get_file_type(ImageName_A);
    1882     par_civ1.ImageWidth=size(Data.A,2);
    1883     par_civ1.ImageHeight=size(Data.A,1);
    1884     par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
    1885     par_civ1.FrameIndexA=num2str(i1);
    1886     par_civ1.FrameIndexB=num2str(i2);
    1887     Param.Civ1=par_civ1;
     1724    [Data,Param.Civ1]=get_param_civ1(handles);
    18881725    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
    18891726    hview_field=view_field(Data); %view the image in the GUI view_field
    … …  
    18931730    ViewData=get(hview_field,'UserData');
    18941731    ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field
    1895     ViewData.PlotAxes.B=imread(ImageName_B);%store the second image in the UserData of the GUI view_field
     1732    ViewData.PlotAxes.B=imread(Param.Civ1.ImageName_B);%store the second image in the UserData of the GUI view_field
    18961733    ViewData.PlotAxes.X=Grid.Civ1_X; %keep the set of points in memeory
    18971734    ViewData.PlotAxes.Y=Grid.Civ1_Y;
    … …  
    19161753        end
    19171754    end
    1918 end
    1919 
    1920 %------------------------------------------------------------------------
    1921 %----function introduced for the correlation window figure, activated by deleting this window
    1922 function closeview_field(gcbo,eventdata)
    1923 %------------------------------------------------------------------------
    1924 hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
    1925 if ~isempty(hview_field)
    1926     delete(hview_field)
    1927 end
    1928 
    1929 %------------------------------------------------------------------------
    1930 % --- Executes on button press in CheckThreshold.
    1931 function CheckThreshold_Callback(hObject, eventdata, handles)
    1932 %------------------------------------------------------------------------
    1933 huipanel=get(hObject,'parent');
    1934 obj(1)=findobj(huipanel,'Tag','num_MinIma');
    1935 obj(2)=findobj(huipanel,'Tag','num_MaxIma');
    1936 obj(3)=findobj(huipanel,'Tag','title_Threshold');
    1937 if get(hObject,'Value')
    1938     set(obj,'Visible','on')
    1939 else
    1940     set(obj,'Visible','off')
    1941 end
    1942 
    1943 
     1755else
     1756    hview_field=findobj(allchild(0),'Tag','view_field'); %view the image in the GUI view_field
     1757    if ~isempty(hview_field)
     1758        delete(hview_field)
     1759    end     
     1760end
     1761
     1762% --------------------------------------------------------------------
     1763% --- Executes on button press in TestPatch1.
     1764% --------------------------------------------------------------------
     1765function TestPatch1_Callback(hObject, eventdata, handles)
     1766
     1767if get(handles.TestPatch1,'Value')
     1768    if get(handles.CheckCiv1,'Value')
     1769        if ~get(handles.CheckFix1,'Value')
     1770            msgbox_uvmat('ERROR','perform FIX1 before testing Patch1')
     1771            return
     1772        end
     1773        set(handles.TestPatch1,'BackgroundColor',[1 1 0])
     1774        drawnow
     1775        [Data,Param.Civ1]=get_param_civ1(handles);
     1776        Param.Fix1=read_GUI(handles.Fix1);
     1777        [Data,errormsg]=civ_matlab(Param);% get the civ1 results
     1778        errormsg=struct2nc('test_civ1.nc',Data);
     1779        InputFile='test_civ1.nc';
     1780        if ~isempty(errormsg)
     1781            msgbox_uvmat('ERROR',['error in temporary file writing: ' errormsg])
     1782            return
     1783        end
     1784    else
     1785        hseries=findobj(allchild(0),'Tag','series');
     1786        hhseries=guidata(hseries);
     1787        InputTable=get(hhseries.InputTable,'Data');
     1788        if ~strcmp(InputTable{1,5},'.nc');
     1789            msgbox_uvmat('ERROR', 'To test patch, first perform Civ1 and Fix1, then open the resulting netcdf file with ''series''')
     1790            return
     1791        end
     1792        set(handles.TestPatch1,'BackgroundColor',[1 1 0])
     1793        drawnow       
     1794        ref_i=str2double(get(handles.ref_i,'String'));
     1795        if strcmp(get(handles.ref_j,'Visible'),'on')
     1796            ref_j=str2double(get(handles.ref_j,'String'));
     1797        else
     1798            ref_j=1;%default
     1799        end
     1800        PairString=get(hhseries.PairString,'Data');
     1801        [i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString{1});
     1802        InputFile=fullfile_uvmat(InputTable{1,1},InputTable{1,2},InputTable{1,3},InputTable{1,5},InputTable{1,4},...
     1803            i1,i2,j1,j2);
     1804    end
     1805    Param=[];
     1806    Param.Patch1=read_GUI(handles.Patch1);
     1807    Param.Patch1.CivFile=InputFile;
     1808    SmoothingParam=(Param.Patch1.FieldSmooth/10)*2.^(1:7);%scan the smoothing param from 1/10 to 12.8 current value
     1809    Data=nc2struct(InputFile);
     1810    NbGood=numel(find(Data.Civ1_FF==0));
     1811    for irho=1:7
     1812        Param.Patch1.FieldSmooth=SmoothingParam(irho);
     1813        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
     1814        if ~isempty(errormsg)
     1815            msgbox_uvmat('ERROR',errormsg)
     1816            return
     1817        end
     1818        ind_good=find(Data.Civ1_FF==0);
     1819        Civ1_U_Diff=Data.Civ1_U(ind_good)-Data.Civ1_U_smooth(ind_good);
     1820        Civ1_V_Diff=Data.Civ1_V(ind_good)-Data.Civ1_V_smooth(ind_good);
     1821        DiffVel(irho)=sqrt(mean(Civ1_U_Diff.*Civ1_U_Diff+Civ1_V_Diff.*Civ1_V_Diff));
     1822        NbExclude(irho)=(NbGood-numel(ind_good))/NbGood;
     1823    end
     1824    figure
     1825    semilogx(SmoothingParam,DiffVel,'b',SmoothingParam,NbExclude,'r')
     1826    grid on
     1827    legend('rms velocity diff. Patch1-Civ1 (pixels)','proportion of excluded vectors (between 0 to 1)')
     1828    XLabel('smoothing parameter')
     1829    YLabel('smoothing effect')
     1830    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
     1831else
     1832    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
     1833    if ~isempty(corrfig)
     1834        delete(corrfig)
     1835    end
     1836    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
     1837    if ~isempty(hview_field)
     1838        delete(hview_field)
     1839    end
     1840end
     1841
     1842
     1843% --- Executes on button press in TestCiv2.
     1844function TestCiv2_Callback(hObject, eventdata, handles)
    19441845
    19451846
    … …  
    19811882end
    19821883
    1983 % --- Executes on button press in TestPatch1.
    1984 function TestPatch1_Callback(hObject, eventdata, handles)
    1985 set(handles.TestPatch1,'BackgroundColor',[1 1 0])
    1986 drawnow
    1987 if get(handles.TestPatch1,'Value')
    1988     ref_i=str2double(get(handles.ref_i,'String'));
    1989     if strcmp(get(handles.ref_j,'Visible'),'on')
    1990         ref_j=str2double(get(handles.ref_j,'String'));
    1991     else
    1992         ref_j=1;%default
    1993     end
    1994     filecell=set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);   
    1995     Data.ListVarName={'ny','nx','A'};
    1996     Data.VarDimName= {'ny','nx',{'ny','nx'}};   
    1997     param_patch1=read_GUI(handles.Patch1);
    1998     param_patch1.CivFile=filecell.nc.civ1{1};
    1999     Param.Patch1=param_patch1;
    2000     for irho=1:7
    2001         [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
    2002         if ~isempty(errormsg)
    2003             msgbox_uvmat('ERROR',errormsg)
    2004             return
    2005         end
    2006         SmoothingParam(irho)=Param.Patch1.FieldSmooth;
    2007         Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
    2008         Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
    2009         DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff));
    2010         NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff);
    2011         Param.Patch1.SmoothingParam=2*Param.Patch1.FieldSmooth;
    2012     end
    2013     figure
    2014     plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
    2015     set(handles.TestPatch1,'BackgroundColor',[1 0 0])
    2016 else
    2017     corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
    2018     if ~isempty(corrfig)
    2019         delete(corrfig)
    2020     end
    2021     hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
    2022     if ~isempty(hview_field)
    2023         delete(hview_field)
    2024     end
    2025 end
    2026 
    2027 
    2028 % --- Executes on button press in TestCiv2.
    2029 function TestCiv2_Callback(hObject, eventdata, handles)
    2030 
    2031 
    2032 
    2033 function num_OriginIndex_Callback(hObject, eventdata, handles)
    2034 % hObject    handle to num_OriginIndex (see GCBO)
    2035 % eventdata  reserved - to be defined in a future version of MATLAB
    2036 % handles    structure with handles and user data (see GUIDATA)
    2037 
    2038 % Hints: get(hObject,'String') returns contents of num_OriginIndex as text
    2039 %        str2double(get(hObject,'String')) returns contents of num_OriginIndex as a double
    2040 
    2041 
    2042 % --- Executes during object creation, after setting all properties.
    2043 function num_OriginIndex_CreateFcn(hObject, eventdata, handles)
    2044 % hObject    handle to num_OriginIndex (see GCBO)
    2045 % eventdata  reserved - to be defined in a future version of MATLAB
    2046 % handles    empty - handles not created until after all CreateFcns called
    2047 
    2048 % Hint: edit controls usually have a white background on Windows.
    2049 %       See ISPC and COMPUTER.
    2050 if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    2051     set(hObject,'BackgroundColor','white');
    2052 end
    20531884
    20541885%------------------------------------------------------------------------
    … …  
    20571888    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
    20581889%------------------------------------------------------------------------
    2059 % i1_series=i_series;% set of first image indexes
    2060 % i2_series=i_series;
    2061 % j1_series=ones(size(i_series));% set of first image numbers
    2062 % j2_series=ones(size(i_series));
    2063 % check_bounds=false(size(i_series));
    20641890ind1='';
    20651891ind2='';
    … …  
    20921918    end
    20931919end
    2094 % if strcmp (mode,'Di')
    2095 %     i1_series=i_series-ind1;% set of first image numbers
    2096 %     i2_series=i_series+ind2;
    2097 %      check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
    2098 %     if isempty(j_series)
    2099 %         NomTypeNc='_1-2';
    2100 %     else
    2101 %         j1_series=j_series;
    2102 %         j2_series=j_series;
    2103 %         NomTypeNc='_1-2_1';
    2104 %     end
    2105 % elseif strcmp (mode,'Dj')
    2106 %     j1_series=j_series-ind1;
    2107 %     j2_series=j_series+ind2;
    2108 %     check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
    2109 %     NomTypeNc='_1_1-2';
    2110 % else  %bursts
    2111 %     j1_series=ind1*ones(size(i_series));
    2112 %     j2_series=ind2*ones(size(i_series));
    2113 % end
     1920
     1921%------------------------------------------------------------------------
     1922% --- fill civ_input with the parameters retrieved from an input Civ file
     1923%------------------------------------------------------------------------
     1924function fill_civ_input(Data,handles)
     1925
     1926%% Civ param
     1927% lists of parameters to enter
     1928ListParamNum={'CorrBoxSize','SearchBoxSize','SearchBoxShift','Dx','Dy','Dz','MinIma','MaxIma'};% list of numerical values (to transform in strings)
     1929ListParamValue={'CorrSmooth','CheckGrid','CheckMask','CheckThreshold'};
     1930ListParamString={'Grid','Mask'};
     1931% CorrSmooth ??
     1932option={'Civ1','Civ2'};
     1933for ichoice=1:2
     1934    if isfield(Data,[option{ichoice} '_CorrBoxSize'])
     1935        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
     1936    end
     1937end
     1938
     1939%% Fix param
     1940option={'Fix1','Fix2'};
     1941for ichoice=1:2
     1942    if isfield(Data,[option{ichoice} '_CheckFmin2'])
     1943        ListParamNum={'MinVel','MaxVel','MinCorr'};% list of numerical values (to transform in strings)
     1944        ListParamValue={'CheckFmin2','CheckF3','CheckF4'};
     1945        ListParamString={'ref_fix_1'};
     1946        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
     1947    end
     1948end
     1949
     1950%% Patch param
     1951option={'Patch1','Patch2'};
     1952for ichoice=1:2
     1953    if isfield(Data,[option{ichoice} '_FieldSmooth'])
     1954        ListParamNum={'FieldSmooth','MaxDiff','SubDomainSize'};% list of numerical values (to transform in strings)
     1955        ListParamValue={};
     1956        ListParamString={};
     1957        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
     1958    end
     1959end
     1960%------------------------------------------------------------------------
     1961% --- fill a panel of civ_input with the parameters retrieved from an input Civ file
     1962%------------------------------------------------------------------------
     1963function fill_panel(Data,handles,panel,ListParamNum,ListParamValue,ListParamString)
     1964children=get(handles.(panel),'children');%handles of the children of the input GUI with handle 'GUI_handle'
     1965handles_panel=[];
     1966for ichild=1:numel(children)
     1967    if ~isempty(get(children(ichild),'tag'))
     1968        handles_panel.(get(children(ichild),'tag'))=children(ichild);
     1969    end
     1970end
     1971for ilist=1:numel(ListParamNum)
     1972    ParamName=ListParamNum{ilist};
     1973    CivParamName=[panel '_' ParamName];
     1974    if isfield(Data,CivParamName)
     1975        for icoord=1:numel(Data.(CivParamName))
     1976            if numel(Data.(CivParamName))>1
     1977                Tag=['num_' ParamName '_' num2str(icoord)];
     1978            else
     1979                Tag=['num_' ParamName];
     1980            end
     1981            if isfield(handles_panel,Tag)
     1982                set(handles_panel.(Tag),'String',num2str(Data.(CivParamName)(icoord)))
     1983                set(handles_panel.(Tag),'Visible','on')
     1984            end
     1985        end
     1986    end
     1987end
     1988for ilist=1:numel(ListParamValue)
     1989    ParamName=ListParamValue{ilist};
     1990    CivParamName=[panel '_' ParamName];
     1991    if strcmp(ParamName,'CorrSmooth')
     1992        ParamName=['num_' ParamName];
     1993    end
     1994    if isfield(Data,CivParamName)
     1995        if isfield(handles_panel,ParamName)
     1996            set(handles_panel.(ParamName),'Value',Data.(CivParamName))
     1997        end
     1998    end
     1999end
     2000for ilist=1:numel(ListParamString)
     2001    ParamName=ListParamString{ilist};
     2002    CivParamName=[panel '_' ParamName];
     2003    if isfield(Data,CivParamName)
     2004        if isfield(handles_panel,ParamName)
     2005            set(handles_panel.(ParamName),'String',Data.(CivParamName))
     2006        end
     2007    end
     2008end
     2009
     2010
     2011% % --- Executes on key press with focus on civ_input and none of its controls.
     2012 function keyboard_callback(hObject,eventdata,handles)
     2013set(handles.ConfigSource,'String','NEW')% indicate that param have been modified
     2014
     2015%------------------------------------------------------------------------
     2016function [Data,par_civ1]=get_param_civ1(handles)
     2017
     2018 ref_i=str2double(get(handles.ref_i,'String'));% read reference i index
     2019 if strcmp(get(handles.ref_j,'Visible'),'on')
     2020     ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant
     2021 else
     2022     ref_j=1;%default j index
     2023 end
     2024 Data.ListVarName={'ny','nx','A'};
     2025 Data.VarDimName= {'ny','nx',{'ny','nx'}};
     2026 hseries=findobj(allchild(0),'Tag','series');
     2027 hhseries=guidata(hseries);
     2028 InputTable=get(hhseries.InputTable,'Data');
     2029 ind_A=1;
     2030 if strcmp(InputTable{1,5},'.nc');
     2031     ind_A=2;
     2032 end
     2033 list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
     2034 PairString=list_pair{get(handles.ListPairCiv1,'Value')};
     2035 [ind1,ind2,mode]=find_pair_indices(PairString,ref_i,ref_j);%,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
     2036 switch mode
     2037     case 'Di'
     2038         i1=ref_i-ind1;
     2039         i2=ref_i+ind2;
     2040         j1=ref_j;
     2041         j2=ref_j;
     2042     case 'Dj'
     2043         i1=ref_i;
     2044         i2=ref_i;
     2045         j1=ref_j-ind1;
     2046         j2=ref_j+ind2;
     2047     case 'burst'
     2048         i1=ref_i;
     2049         i2=ref_i;
     2050         j1=ind1;
     2051         j2=ind2;
     2052 end
     2053 ImageName_A=fullfile_uvmat(InputTable{ind_A,1},InputTable{ind_A,2},InputTable{ind_A,3},InputTable{ind_A,5},InputTable{ind_A,4},...
     2054     i1,[],j1);
     2055 ImageName_B=fullfile_uvmat(InputTable{ind_A,1},InputTable{ind_A,2},InputTable{ind_A,3},InputTable{ind_A,5},InputTable{ind_A,4},...
     2056     i2,[],j2);
     2057 Data.A=imread(ImageName_A); % read the first image
     2058 if ndims(Data.A)==3 %case of color image
     2059     Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
     2060 end
     2061 Data.ny=[size(Data.A,1) 1];
     2062 Data.nx=[1 size(Data.A,2)];
     2063 Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly
     2064 par_civ1=read_GUI(handles.Civ1);
     2065 par_civ1.FileTypeA=get_file_type(ImageName_A);
     2066 par_civ1.ImageWidth=size(Data.A,2);
     2067 par_civ1.ImageHeight=size(Data.A,1);
     2068 par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
     2069 par_civ1.FrameIndexA=num2str(i1);
     2070 par_civ1.FrameIndexB=num2str(i2);
     2071 par_civ1.ImageName_B=ImageName_B;
     2072 
     2073
     2074% handles    structure with handles and user data (see GUIDATA)

  • trunk/src/series/civ_series.m

    r768 r774  
    5252    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
    5353    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
    54     if strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
     54    if isfield(Data,'ActionInput') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
    5555        Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input)
    5656    end

  • trunk/src/series/sub_background.m

    r716 r774  
    102102        NbSlice=Param.IndexRange.NbSlice;
    103103    end
    104     %nbview=numel(i1_series);%number of input file series (lines in InputTable)
    105     nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)%A CORRIGER !!!!!!!
    106     nbfield_i=size(i1_series{1},2); %nb of fields for the i index
     104    incr_j=1;%default
     105    if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j)
     106        incr_j=Param.IndexRange.incr_j;
     107    end
     108    if isempty(first_j)||isempty(last_j)
     109        nbfield_j=1;
     110    else
     111        nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices)
     112    end
     113    incr_i=1;%default
     114    first_i=1;last_i=1;incr_i;%default
     115    if isfield(Param.IndexRange,'first_i'); last_i=Param.IndexRange.first_i; end   
     116    if isfield(Param.IndexRange,'last_i'); last_i=Param.IndexRange.last_j; end
     117    if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i)
     118        incr_i=Param.IndexRange.incr_i;
     119    end
     120    nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices)
    107121    nbfield=nbfield_j*nbfield_i; %total number of fields
    108122    nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
    … …  
    175189NomType=Param.InputTable(:,4);
    176190FileExt=Param.InputTable(:,5);
     191hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
    177192[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
     193if ~isempty(hdisp),delete(hdisp),end;
    178194%%%%%%%%%%%%
    179195    % The cell array filecell is the list of input file names, while
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