Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 1019) +++ /trunk/src/series/civ_input.m (revision 1020) @@ -60,8 +60,6 @@ set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display) set(hObject,'WindowKeyPressFcn',{@keyboard_callback,handles})%set keyboard action function -%set(hObject,'KeyPressFcn',{@KeyPressFcn,handles})%set keyboard action function set(handles.ref_i,'KeyPressFcn',{@ref_i_KeyPressFcn,handles})%set keyboard action function set(handles.ref_j,'KeyPressFcn',{@ref_i_KeyPressFcn,handles})%set keyboard action function -%set(hObject,'WindowKeyPressFcn',{'keyboard_callback',handles})%set keyboard action function hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series' hhseries=guidata(hseries); %handles of the elements in 'series' @@ -220,8 +218,5 @@ if isfield(Param.IndexRange,'TimeUnit')&&~isempty(Param.IndexRange.TimeUnit) TimeUnit=Param.IndexRange.TimeUnit; -end -% if isfield(SeriesData,'TimeSource') -% set(handles.TimeSource,'String',SeriesData.TimeSource) -% end +end if isfield(SeriesData,'GeometryCalib') tsai=SeriesData.GeometryCalib; @@ -317,4 +312,8 @@ end + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + set(handles.PairIndices,'Visible','off') + end + %% set the menu and default choice of civ pairs if ~isfield(Param.IndexRange,'first_j')||isequal(MaxIndex_j,MinIndex_j)% no possibility of j pairs @@ -668,9 +667,7 @@ OriginIndex='off'; PairIndices='off'; -DoubleInputSeries='off'; switch option case 'PIV' - PairIndices='on';% needs to define index pairs for PIV - + PairIndices='on';% needs to define index pairs for PIV case 'PIV volume' PairIndices='on';% needs to define index pairs for PIV @@ -680,18 +677,15 @@ case 'displacement' OriginIndex='on';%define a frame origin for displacement -% case 'shift' -% if numel(ImageType)==1 -% fileinput=uigetfile_uvmat('pick a second file series for synchronous shift',InputTable{check_nc+1}); -% if ~isempty(fileinput) -% series( 'display_file_name',hhseries,fileinput,'append') -% end -% -% -% end end set(handles.num_OriginIndex,'Visible',OriginIndex) set(handles.OriginIndex_title,'Visible',OriginIndex) +set(handles.CheckRefFile,'Visible',OriginIndex) +set(handles.RefFile,'Visible',OriginIndex) set(handles.PairIndices,'Visible',PairIndices) -ListPairMode_Callback(hObject, eventdata, handles) +ListPairMode_Callback(hObject,eventdata,handles) +if strcmp(OriginIndex,'on') + set(handles.CheckRefFile,'Value',1) + CheckRefFile_Callback(hObject,eventdata,handles) +end @@ -708,5 +702,5 @@ compare=compare_list{val}; if strcmp(compare,'displacement')||strcmp(compare,'shift') - mode='displacement'; + mode_selected='displacement'; else mode_list=get(handles.ListPairMode,'String'); @@ -718,5 +712,5 @@ mode_value=1; end - mode=mode_list{mode_value}; + mode_selected=mode_list{mode_value}; end % displ_num=[];%default @@ -734,5 +728,5 @@ % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices % are relative to the reference indices ref_i and ref_j respectively. -if isequal(mode,'pair j1-j2') +if isequal(mode_selected,'pair j1-j2') dt=1; displ=''; @@ -764,5 +758,5 @@ displ_num(4,:)=0; enable_j(handles, 'off') -elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') +elseif isequal(mode_selected,'series(Dj)') %| isequal(mode,'st_series(Dj)') index=1:200; displ_num(1,index)=-floor(index/2); @@ -770,5 +764,5 @@ displ_num(3:4,index)=zeros(2,200); enable_j(handles, 'on') -elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') +elseif isequal(mode_selected,'series(Di)') %| isequal(mode,'st_series(Di)') % index=1:200; % displ_num(1:2,index)=zeros(2,200); @@ -781,5 +775,5 @@ enable_j(handles, 'off') end -elseif isequal(mode,'displacement')%the pairs have the same indices +elseif isequal(mode_selected,'displacement')%the pairs have the same indices displ_num(1,1)=0; displ_num(2,1)=0; @@ -855,7 +849,7 @@ mode_list=get(handles.ListPairMode,'String'); mode_value=get(handles.ListPairMode,'Value'); -mode=mode_list{mode_value}; +mode_selected=mode_list{mode_value}; errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files -if isequal(mode,'series(Di)') || ...% we do patch2 only +if isequal(mode_selected,'series(Di)') || ...% we do patch2 only (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) errormsg=find_netcpair_civ( handles,2); @@ -872,28 +866,5 @@ % %------------------------------------------------------------------------ -% function ref_j_Callback(hObject, eventdata, handles) -% %------------------------------------------------------------------------ -% mode_list=get(handles.ListPairMode,'String'); -% mode_value=get(handles.ListPairMode,'Value'); -% mode=mode_list{mode_value}; -% errormsg=''; -% if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)') -% errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files -% end -% if isequal(mode,'series(Dj)') || ... -% (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) -% errormsg=find_netcpair_civ(handles,2); -% end -% if ~isempty(errormsg) -% msgbox_uvmat('ERROR',errormsg) -% end -% -% function ref_j_KeyPressFcn(hObject, eventdata, handles) -% set(handles.ref_j,'BackgroundColor',[1 0 1]) -%------------------------------------------------------------------------ -% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of -% the field series set by MinIndex_i, incr, last_i -% index=1: look for pairs for civ1 -% index=2: look for pairs for civ2 + function errormsg=find_netcpair_civ(handles,index) %------------------------------------------------------------------------ @@ -907,4 +878,5 @@ val=get(handles.ListCompareMode,'Value'); compare=compare_list{val}; +mode_selected='displacement'; if ~strcmp(compare,'displacement')%||strcmp(compare,'shift') @@ -917,5 +889,5 @@ return end - mode=mode_list{mode_value}; + mode_selected=mode_list{mode_value}; end nom_type_ima=CivInputData.NomTypeIma; @@ -935,5 +907,5 @@ ref_i=str2double(get(handles.ref_i,'String')); ref_j=[]; -if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') +if isequal(mode_selected,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') ref_j=0; elseif strcmp(get(handles.ref_j,'Visible'),'on') @@ -955,5 +927,5 @@ %% determine the menu display in .ListPairCiv1 -switch mode +switch mode_selected case 'series(Di)' for ipair=1:nbpair @@ -995,6 +967,4 @@ end case 'pair j1-j2'%case of pairs -% MinIndex_j=CivInputData.MinIndex_j; -% MaxIndex_j=min(CivInputData.MaxIndex_j,10);%limitate the number of pairs to 10x10 MinIndex_j=str2num(get(handles.MinIndex_j,'String')); MaxIndex_j=str2num(get(handles.MaxIndex_j,'String')); @@ -1131,42 +1101,4 @@ end if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax)) -% list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs -% index=get(handles.ListPairCiv1,'Value'); -% pair_string=list_pair{index}; -% time=get(handles.TimeSource,'UserData'); %get the set of times -% pxcm=get(handles.SearchRange,'UserData'); -% mode_list=get(handles.ListPairMode,'String'); -% mode_value=get(handles.ListPairMode,'Value'); -% mode=mode_list{mode_value}; -% if isequal (mode, 'series(Di)' ) -% ref_i=str2double(get(handles.ref_i,'String')); -% num1=ref_i-floor(index/2);% first image numbers -% num2=ref_i+ceil(index/2); -% num_a=1; -% num_b=1; -% elseif isequal (mode, 'series(Dj)') -% num1=1; -% num2=1; -% ref_j=str2double(get(handles.ref_j,'String')); -% num_a=ref_j-floor(index/2);% first image numbers -% num_b=ref_j+ceil(index/2); -% elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) -% ref_i=str2double(get(handles.ref_i,'String')); -% num1=ref_i; -% num2=ref_i; -% r=regexp(pair_string,'(?(Di=)|(Dj=)) -*(?\d+)\|(?\d+)','names'); -% if isempty(r) -% r=regexp(pair_string,'(?\d+)(?-)(?\d+)','names'); -% end -% num_a=str2num(r.num1); -% num_b=str2num(r.num2); -% end -% dt=time(num2+1,num_b+1)-time(num1+1,num_a+1); -% ibx=str2double(get(handles.num_CorrBoxSize_1,'String')); -% iby=str2double(get(handles.num_CorrBoxSize_2,'String')); -% umin=dt*pxcm*umin; -% umax=dt*pxcm*umax; -% vmin=dt*pxcm*vmin; -% vmax=dt*pxcm*vmax; shiftx=round((umin+umax)/2); shifty=round((vmin+vmax)/2); @@ -1555,9 +1487,5 @@ ind_A=2; end -% [nbslice, flag_mask]=get_mask(InputTable{ind_A,1},handles);% look for a mask with appropriate name -% if isequal(flag_mask,1) -% filemask=[num2str(nbslice) 'mask']; -% testmask=1; -% else % browse for a mask + % browse for a mask filemask= uigetfile_uvmat('pick a mask image file:',InputTable{ind_A,1},'image'); [FilePath,FileName,Ext]=fileparts(filemask); @@ -1570,6 +1498,5 @@ if ~isempty(filemask) testmask=1; - end -% end + end end if testmask @@ -2194,5 +2121,5 @@ %'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature %--------------------------------------------------------------------- -function NomTypeNc=nomtype2pair(NomTypeIma,mode) +function NomTypeNc=nomtype2pair(NomTypeIma,mode_selected) %--------------------------------------------------------------------- % OUTPUT: @@ -2203,5 +2130,5 @@ NomTypeNc=NomTypeIma;%default -switch mode +switch mode_selected case 'pair j1-j2' if ~isempty(regexp(NomTypeIma,'a$')) @@ -2232,5 +2159,5 @@ %------------------------------------------------------------------------ % --- determine the list of index pairs of processing file -function [ind1,ind2,mode]=... +function [ind1,ind2,mode_selected]=... find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) %------------------------------------------------------------------------ @@ -2239,9 +2166,9 @@ r=regexp(str_civ,'^\D(?[i|j])=( -| )(?\d+)\|(?\d+)','names'); if ~isempty(r) - mode=['D' r.ind]; + mode_selected=['D' r.ind]; ind1=stra2num(r.num1); ind2=stra2num(r.num2); else - mode='burst'; + mode_selected='burst'; r=regexp(str_civ,'^j= (?[a-z])-(?[a-z])','names'); if ~isempty(r) @@ -2402,4 +2329,18 @@ function CheckCiv3_Callback(hObject, eventdata, handles) +% --- Executes on button press in CheckRefFile. +function CheckRefFile_Callback(hObject, eventdata, handles) + + hseries=findobj(allchild(0),'Tag','series'); + hhseries=guidata(hseries); + InputTable=get(hhseries.InputTable,'Data'); + InputFile=fullfile(InputTable{1,1},InputTable{1,2},[InputTable{1,3} InputTable{1,5}]); + % browse for a reference file for displacement + fileref= uigetfile_uvmat('pick a reference image file:',InputFile); + if ~isempty(fileref) + set(handles.RefFile,'String',fileref) + set(handles.ConfigSource,'String','NEW') + set(handles.ConfigSource,'BackgroundColor',[1 0 1]) + end %------------------------------------------------------------------------ @@ -2414,25 +2355,2 @@ drawnow end - - - -function num_NbSlice_Callback(hObject, eventdata, handles) -% hObject handle to num_NbSlice (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% Hints: get(hObject,'String') returns contents of num_NbSlice as text -% str2double(get(hObject,'String')) returns contents of num_NbSlice as a double - - -% --- Executes during object creation, after setting all properties. -function num_NbSlice_CreateFcn(hObject, eventdata, handles) -% hObject handle to num_NbSlice (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles empty - handles not created until after all CreateFcns called - -% Hint: edit controls usually have a white background on Windows. -% See ISPC and COMPUTER. -if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) - set(hObject,'BackgroundColor','white'); -end Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 1019) +++ /trunk/src/series/civ_series.m (revision 1020) @@ -60,7 +60,4 @@ Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) - % if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices')&& strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') - % Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input) - % end Data.NbSlice='off'; %nbre of slices ('off' by default) Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) @@ -73,5 +70,5 @@ Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) - if isequal(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') + if isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') if isfield(Data.ActionInput.PairIndices,'ListPairCiv2') str_civ=Data.ActionInput.PairIndices.ListPairCiv2; @@ -133,7 +130,7 @@ iview_A=2;% the second line is used for the input images of Civ2 end - if strcmp(Param.ActionInput.ListCompareMode,'shift') - iview_B=iview_A+1; % the second image series is on the next line of the input table - end +% if strcmp(Param.ActionInput.ListCompareMode,'shift') +% iview_B=iview_A+1; % the second image series is on the next line of the input table +% end if iview_A~=0 RootPath_A=Param.InputTable{iview_A,1}; @@ -180,24 +177,28 @@ case 'displacement' i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); - i2_series_Civ1=i1_series{1};i2_series_Civ2=i1_series{1}; - j1_series_Civ1=ones(size(i1_series{1}));% first j index is 1 - if isempty(j1_series_Civ1) - j2_series_Civ1=ones(size(i1_series{1})); + i1_series_Civ2=i1_series_Civ1; + i2_series_Civ1=i1_series{1}; + i2_series_Civ2=i1_series{1}; + j1_series_Civ1=[];% no j index variation for the ref image + j1_series_Civ2=[]; + if isempty(j1_series{1}) + j2_series_Civ1=ones(size(i1_series_Civ1)); else - j2_series_Civ1=j1_series_Civ1; - end - i1_series_Civ2=i1_series_Civ1; - j1_series_Civ2=j1_series_Civ1; + j2_series_Civ1=j1_series{1};% if j index exist + end j2_series_Civ2=j2_series_Civ1; - NomTypeNc=Param.InputTable{1,4}; + NomTypeNc='_1'; case 'PIV volume' % TODO, TODO end - if isempty(j1_series_Civ1) + %determine frame indices for input with movie or other multiframe input file + if isempty(j1_series_Civ1)% simple movie with index i FrameIndex_A_Civ1=i1_series_Civ1; FrameIndex_B_Civ1=i2_series_Civ1; j1_series_Civ1=ones(size(i1_series_Civ1)); + if strcmp(Param.ActionInput.ListCompareMode,'PIV') j2_series_Civ1=ones(size(i1_series_Civ1)); - else + end + else % movie for each burst or volume (index j) FrameIndex_A_Civ1=j1_series_Civ1; FrameIndex_B_Civ1=j2_series_Civ1; @@ -211,5 +212,7 @@ FrameIndex_B_Civ2=i2_series_Civ2; j1_series_Civ2=ones(size(i1_series_Civ2)); + if strcmp(Param.ActionInput.ListCompareMode,'PIV') j2_series_Civ2=ones(size(i1_series_Civ2)); + end else FrameIndex_A_Civ2=j1_series_Civ2; @@ -227,5 +230,4 @@ NbField=numel(i1_series_Civ1); elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 - NbField=numel(i1_series_Civ2); else @@ -233,6 +235,4 @@ end - - %% Output directory OutputDir=''; @@ -257,5 +257,4 @@ if isfield(XmlData,'Time') Time=XmlData.Time; - TimeSource='xml'; end if isfield(XmlData,'Camera') @@ -271,6 +270,4 @@ end end - - end @@ -342,8 +339,12 @@ disp('civ1 started') end - par_civ1=Param.ActionInput.Civ1; + par_civ1=Param.ActionInput.Civ1;% parameters for civ1 if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) try + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + ImageName_A=Param.ActionInput.RefFile; + else ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); + end if strcmp(FileExt_A,'.nc')% case of input images in format netcdf FieldName_A=Param.InputFields.FieldName; @@ -351,5 +352,5 @@ par_civ1.ImageA=DataIn.(FieldName_A); else % usual image formats for image A - if isempty(FileType_A) + if isempty(FileType_A)% open the image object if not already done in case of movie input [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); FileType_A=FileInfo_A.FileType; @@ -357,6 +358,4 @@ Time=zeros(FileInfo_A.NumberOfFrames+1,2); Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; - TimeSource='video'; - ColorType='truecolor'; end if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default @@ -596,19 +595,9 @@ par_civ2.ImageA=[]; par_civ2.ImageB=[]; - % i1_civ2=i1_series_Civ2(ifield); - % i2_civ2=i1_civ2; - % if ~isempty(i2_series_Civ2) - % i2_civ2=i2_series_Civ2(ifield); - % end - % j1_civ2=1; - % if ~isempty(j1_series_Civ2) - % j1_civ2=j1_series_Civ2(ifield); - % end - % j2_civ2=i1_civ2; - % if ~isempty(j2_series_Civ2) - % j2_civ2=j2_series_Civ2(ifield); - % end + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + ImageName_A_Civ2=Param.ActionInput.RefFile; + else ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); - + end if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) par_civ2.ImageA=par_civ1.ImageA; @@ -622,9 +611,4 @@ [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); end - % if strcmp(Param.ActionInput.ListCompareMode,'PIV') - % ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2); - % else % displacement - % ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2,[],j2); - % end par_civ2.ImageWidth=FileInfo_A.Width; par_civ2.ImageHeight=FileInfo_A.Height;