Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 760) +++ /trunk/src/series/civ_input.m (revision 761) @@ -143,8 +143,8 @@ iview_image=2;%line # for the input images case 'civxdata'% case of civx data, - NomTypeNc=NomTypeInput; - ind_opening=FileInfo.CivStage; - set(handles.Program,'Value',3) %select Cix by default msgbox_uvmat('ERROR','old civX convention, use the GUI civ') + return + otherwise + msgbox_uvmat('ERROR','civ_series needs images or civ data as input') return end Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 760) +++ /trunk/src/series/civ_series.m (revision 761) @@ -97,5 +97,5 @@ end if isfield(Param,'InputTable') - [tild,i_series,tild,j_series]=get_file_series(Param); + [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); % iview_nc=0;% series index (iview) for an input nc file (for civ2 or patch2) iview_A=0;% series index (iview) for the first image series @@ -107,5 +107,5 @@ end if strcmp(Param.ActionInput.ListCompareMode,'shift') - iview_B=iview_A+1; % the second image series is on the next line of the tinput table + iview_B=iview_A+1; % the second image series is on the next line of the input table end if iview_A~=0 @@ -132,23 +132,36 @@ PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2; end - [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... - find_pair_indices(PairCiv1,i_series{1},j_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); - if ~isempty(PairCiv2) - [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... - find_pair_indices(PairCiv2,i_series{1},j_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); - check_bounds=check_bounds | check_bounds_Civ2; - end - i1_series_Civ1=i1_series_Civ1(~check_bounds); - i2_series_Civ1=i2_series_Civ1(~check_bounds); - j1_series_Civ1=j1_series_Civ1(~check_bounds); - j2_series_Civ1=j2_series_Civ1(~check_bounds); + if iview_A==1% if Civ1 is performed + [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... + find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); + if ~isempty(PairCiv2) + [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... + find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); + check_bounds=check_bounds | check_bounds_Civ2; + end + else% we start from an existing Civ1 file + i1_series_Civ1=i1_series{1}; + i2_series_Civ1=i2_series{1}; + j1_series_Civ1=j1_series{1}; + j2_series_Civ1=j2_series{1}; + NomTypeNc=Param.InputTable{1,4}; + if ~isempty(PairCiv2) + [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... + find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); +% check_bounds=check_bounds | check_bounds_Civ2; + end + end +% i1_series_Civ1=i1_series_Civ1(~check_bounds); +% i2_series_Civ1=i2_series_Civ1(~check_bounds); +% j1_series_Civ1=j1_series_Civ1(~check_bounds); +% j2_series_Civ1=j2_series_Civ1(~check_bounds); case 'displacement' i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i_series{1})); i2_series_Civ1=i_series{1};i2_series_Civ2=i_series{1}; j1_series_Civ1=ones(size(i_series{1}));% first j index is 1 - if isempty(j_series{1}) + if isempty(j1_series_Civ1) j2_series_Civ1=ones(size(i_series{1})); else - j2_series_Civ1=j_series{1}; + j2_series_Civ1=j1_series_Civ1; end i1_series_Civ2=i1_series_Civ1; @@ -170,7 +183,9 @@ NomTypeNc=NomType_A; end - if isempty(j_series{1}) + if isempty(j1_series_Civ1) FrameIndex_A_Civ1=i1_series_Civ1; FrameIndex_B_Civ1=i2_series_Civ1; + j1_series_Civ1=ones(size(i1_series_Civ1)); + j2_series_Civ1=ones(size(i1_series_Civ1)); else FrameIndex_A_Civ1=j1_series_Civ1; @@ -178,9 +193,9 @@ end if ~isempty(PairCiv2) - i1_series_Civ2=i1_series_Civ2(~check_bounds); - i2_series_Civ2=i2_series_Civ2(~check_bounds); - j1_series_Civ2=j1_series_Civ2(~check_bounds); - j2_series_Civ2=j2_series_Civ2(~check_bounds); - if isempty(j_series{1}) +% i1_series_Civ2=i1_series_Civ2(~check_bounds); +% i2_series_Civ2=i2_series_Civ2(~check_bounds); +% j1_series_Civ2=j1_series_Civ2(~check_bounds); +% j2_series_Civ2=j2_series_Civ2(~check_bounds); + if isempty(j1_series_Civ2) FrameIndex_A_Civ2=i1_series_Civ2; FrameIndex_B_Civ2=i2_series_Civ2; @@ -300,9 +315,14 @@ break end + if iview_A==1% if Civ1 is performed + Civ1Dir=OutputDir; + else + Civ1Dir=Param.InputTable{1,2}; + end if strcmp(Param.ActionInput.ListCompareMode,'PIV') - ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... + ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... j1_series_Civ1(ifield),j2_series_Civ1(ifield)); else - ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... + ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... j1_series_Civ1(ifield),j2_series_Civ1(ifield)); end @@ -400,7 +420,6 @@ CivFile=Param.Patch1.CivFile; end - Data=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format - if isfield(Data,'Txt') - errormsg=Data.Txt; + [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format + if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) return @@ -410,5 +429,5 @@ [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file else - Data=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file + [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file end end @@ -526,8 +545,9 @@ NbSubDomain=size(Data.Civ1_SubRange,3); % get the guess from patch1 - for isub=1:NbSubDomain - nbvec_sub=Data.Civ1_NbCentres(isub); - ind_sel=find(GridX>=Data.Civ1_SubRange(1,1,isub) & GridX<=Data.Civ1_SubRange(1,2,isub) & GridY>=Data.Civ1_SubRange(2,1,isub) & GridY<=Data.Civ1_SubRange(2,2,isub)); - epoints = [GridX(ind_sel) GridY(ind_sel)];% coordinates of interpolation sites + for isub=1:NbSubDomain% for each sub-domain of Patch1 + nbvec_sub=Data.Civ1_NbCentres(isub);% nbre of Civ1 vectors in the subdomain + ind_sel=find(par_civ2.Grid(:,1)>=Data.Civ1_SubRange(1,1,isub) & par_civ2.Grid(:,1)<=Data.Civ1_SubRange(1,2,isub) &... + par_civ2.Grid(:,2)>=Data.Civ1_SubRange(2,1,isub) & par_civ2.Grid(:,2)<=Data.Civ1_SubRange(2,2,isub)); + epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap) @@ -552,5 +572,5 @@ par_civ2.SearchBoxSize(2)=2*iby2+9; par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; - par_civ2.Grid=[GridX(nbval>=1)-par_civ2.SearchBoxShift(:,1)/2 GridY(nbval>=1)-par_civ2.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors + par_civ2.Grid=[par_civ2.Grid(nbval>=1,1)-par_civ2.SearchBoxShift(:,1)/2 par_civ2.Grid(nbval>=1,2)-par_civ2.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors if par_civ2.CheckDeformation par_civ2.DUDX=DUDX./nbval; Index: /trunk/src/series/turb_stat.m =================================================================== --- /trunk/src/series/turb_stat.m (revision 760) +++ /trunk/src/series/turb_stat.m (revision 761) @@ -184,5 +184,6 @@ U2Mean_1=0; V2Mean_1=0; -checkgrid=0;% test for a structured grid for input field +Counter_1=0; + %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% for index=1:NbField @@ -201,7 +202,9 @@ Uprev=Field.U; Vprev=Field.V; - end - FF=isnan(Field.U)|Field.U<-60|Field.U>30;% threshold on U + FFprev=Field.FF; + end + FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U DataOut.Counter=DataOut.Counter+ (~FF);% add 1 to the couter for non NaN point + Counter_1=Counter_1+(~FF & ~FFprev); Field.U(FF)=0;% set to 0 the nan values Field.V(FF)=0; @@ -215,4 +218,5 @@ Uprev=Field.U; %store for next iteration Vprev=Field.V; + FFprev=FF; end %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% @@ -224,6 +228,6 @@ V2Mean=V2Mean./DataOut.Counter; % normalize the mean UVMean=UVMean./DataOut.Counter; % normalize the mean -U2Mean_1=U2Mean_1./DataOut.Counter; % normalize the mean -V2Mean_1=V2Mean_1./DataOut.Counter; % normalize the mean +U2Mean_1=U2Mean_1./Counter_1; % normalize the mean +V2Mean_1=V2Mean_1./Counter_1; % normalize the mean DataOut.u2Mean=U2Mean-DataOut.UMean.*DataOut.UMean; % normalize the mean DataOut.v2Mean=V2Mean-DataOut.VMean.*DataOut.VMean; % normalize the mean