%'civ_matlab': Matlab version of the PIV programs CivX % --- call the sub-functions: % civ: PIV function itself % fix: removes false vectors after detection by various criteria % patch: make interpolation-smoothing %------------------------------------------------------------------------ % function [Data,errormsg,result_conv]= civ_uvmat(Param,ncfile) % %OUTPUT % Data=structure containing the PIV results and information on the processing parameters % errormsg=error message char string, default='' % resul_conv: image inter-correlation function for the last grid point (used for tests) % %INPUT: % Param: input images and processing parameters % ncfile: name of a netcdf file to be created for the result (extension .nc) % %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % Copyright 2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % This is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published by % the Free Software Foundation; either version 2 of the License, or % (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (open UVMAT/COPYING.txt) for more details. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA function [Data,errormsg,result_conv]= civ_matlab(Param,ncfile) errormsg=''; Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes Data.Program='civ_matlab'; Data.CivStage=0;%default ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'}; mask=''; maskname='';%default check_civx=0;%default check_civ1=0;%default check_patch1=0;%default %% Civ1 if isfield (Param,'Civ1') check_civ1=1;% test for further use of civ1 results % caluclate velocity data (y and v in indices, reverse to y component) [xtable ytable utable vtable ctable F result_conv errormsg] = civ (Param.Civ1); if ~isempty(errormsg) return end list_param=(fieldnames(Param.Civ1))'; Civ1_param=list_param;%default for ilist=1:length(list_param) Civ1_param{ilist}=['Civ1_' list_param{ilist}]; % eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';']) Data.(['Civ1_' list_param{ilist}])=Param.Civ1.(list_param{ilist}); end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];% {'Civ1_Time','Civ1_Dt'}]; % if exist('ncfile','var')% TEST for use interactively with mouse_motion (no file created) Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};% cell array containing the names of the fields to record Data.VarDimName={'nbvec1','nbvec1','nbvec1','nbvec1','nbvec1','nbvec1'}; Data.VarAttribute{1}.Role='coord_x'; Data.VarAttribute{2}.Role='coord_y'; Data.VarAttribute{3}.Role='vector_x'; Data.VarAttribute{4}.Role='vector_y'; Data.VarAttribute{5}.Role='warnflag'; Data.Civ1_X=reshape(xtable,[],1); Data.Civ1_Y=reshape(Param.Civ1.ImageHeight-ytable+1,[],1); Data.Civ1_U=reshape(utable,[],1); Data.Civ1_V=reshape(-vtable,[],1); Data.Civ1_C=reshape(ctable,[],1); Data.Civ1_F=reshape(F,[],1); Data.CivStage=1; else Data=nc2struct(ncfile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format if ~isempty(Data.absolut_time_T0')%read civx file check_civx=1;% test for old civx data format [Data,vardetect,ichoice]=nc2struct(ncfile);%read the variables in the netcdf file else if isfield(Param,'Fix1') Data=nc2struct(ncfile,ListVarCiv1);%read civ1 data in the existing netcdf file else Data=nc2struct(ncfile,ListVarFix1);%read civ1 and fix1 data in the existing netcdf file end end if isfield(Data,'Txt') msgbox_uvmat('ERROR',Data.Txt) return end end %% Fix1 if isfield (Param,'Fix1') ListFixParam=fieldnames(Param.Fix1); for ilist=1:length(ListFixParam) ParamName=ListFixParam{ilist}; ListName=['Fix1_' ParamName]; eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) eval(['Data.' ListName '=Param.Fix1.' ParamName ';']) end % Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Fix1_WarnFlags','Fix1_TreshCorr','Fix1_TreshVel','Fix1_UpperBoundTest'}]; % Data.Fix1_WarnFlags=Param.Fix1.WarnFlags; % Data.Fix1_ThreshCorr=Param.Fix1.ThreshCorr; % Data.Fix1_ThreshVel=Param.Fix1.ThreshVel; % Data.Fix1_UpperBoundTest=Param.Fix1.UpperBoundTest; if check_civx if ~isfield(Data,'fix') Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix']; Data.fix=1; Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}]; Data.VarDimName=[Data.VarDimName {'nb_vectors'}]; end Data.vec_FixFlag=fix(Param.Fix1,Data.vec_F,Data.vec_C,Data.vec_U,Data.vec_V,Data.vec_X,Data.vec_Y); else Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; Data.VarDimName=[Data.VarDimName {'nbvec1'}]; nbvar=length(Data.ListVarName); Data.VarAttribute{nbvar}.Role='errorflag'; Data.Civ1_FF=fix(Param.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); Data.CivStage=2; end end %% Patch1 if isfield (Param,'Patch1') check_patch1=1; Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; Data.Patch1_Rho=str2double(Param.Patch1.Rho); Data.Patch1_Threshold=str2double(Param.Patch1.Threshold); Data.Patch1_SubDomain=str2double(Param.Patch1.SubDomain); Data.ListVarName=[Data.ListVarName {'Civ1_U_Diff','Civ1_V_Diff','Civ1_X_SubRange','Civ1_Y_SubRange','Civ1_NbSites','Civ1_X_tps','Civ1_Y_tps','Civ1_U_tps','Civ1_V_tps'}]; Data.VarDimName=[Data.VarDimName {'NbVec1','NbVec1',{'NbSubDomain1','Two'},{'NbSubDomain1','Two'},'NbSubDomain1',... {'NbVec1Sub','NbSubDomain1'},{'NbVec1Sub','NbSubDomain1'},{'Nbtps1','NbSubDomain1'},{'Nbtps1','NbSubDomain1'}}]; nbvar=length(Data.ListVarName); Data.VarAttribute{nbvar-1}.Role='vector_x'; Data.VarAttribute{nbvar}.Role='vector_y'; Data.Civ1_U_Diff=zeros(size(Data.Civ1_X)); Data.Civ1_V_Diff=zeros(size(Data.Civ1_X)); if isfield(Data,'Civ1_FF') ind_good=find(Data.Civ1_FF==0); else ind_good=1:numel(Data.Civ1_X); end [Data.Civ1_X_SubRange,Data.Civ1_Y_SubRange,Data.Civ1_NbSites,FFres,Ures, Vres,Data.Civ1_X_tps,Data.Civ1_Y_tps,Data.Civ1_U_tps,Data.Civ1_V_tps]=... patch(Data.Civ1_X(ind_good)',Data.Civ1_Y(ind_good)',Data.Civ1_U(ind_good)',Data.Civ1_V(ind_good)',Data.Patch1_Rho,Data.Patch1_Threshold,Data.Patch1_SubDomain); Data.Civ1_U_Diff(ind_good)=Data.Civ1_U(ind_good)-Ures; Data.Civ1_V_Diff(ind_good)=Data.Civ1_V(ind_good)-Vres; Data.Civ1_FF(ind_good)=FFres; Data.CivStage=3; end %% Civ2 if isfield (Param,'Civ2') par_civ2=Param.Civ2; if ~check_civ1 || ~strcmp(par_civ1.filename_ima_a,par_civ2.filename_ima_a) par_civ2.ImageA=imread(par_civ2.filename_ima_a);%read first image if not already done for civ1 end if ~check_civ1|| ~strcmp(par_civ1.filename_ima_b,par_civ2.filename_ima_b) par_civ2.ImageB=imread(par_civ2.filename_ima_b);%read second image if not already done for civ1 end % stepx=str2double(par_civ2.dx); % stepy=str2double(par_civ2.dy); ibx2=ceil(str2double(par_civ2.ibx)/2); iby2=ceil(str2double(par_civ2.iby)/2); isx2=ibx2+2; isy2=iby2+2; %get the previous guess for displacement if ~check_patch1 [Guess,VelType]=read_civdata(ObjectName,InputField,ParamIn.VelType);%TO DEVELOP else Data.Civ1_U_Diff=zeros(size(Data.Civ1_X)); Data.Civ1_V_Diff=zeros(size(Data.Civ1_X)); if isfield(Data,'Civ1_FF') ind_good=find(Data.Civ1_FF==0); else ind_good=1:numel(Data.Civ1_X); end [Data.Civ1_X_SubRange,Data.Civ1_Y_SubRange,Data.Civ1_NbSites,FFres,Ures, Vres,Data.Civ1_X_tps,Data.Civ1_Y_tps,Data.Civ1_U_tps,Data.Civ1_V_tps]=... patch(Data.Civ1_X(ind_good)',Data.Civ1_Y(ind_good)',Data.Civ1_U(ind_good)',Data.Civ1_V(ind_good)',Data.Patch1_Rho,Data.Patch1_Threshold,Data.Patch1_SubDomain); end % shiftx=str2num(par_civ1.shiftx); % shifty=str2num(par_civ1.shifty); % TO GET shift from par_civ2.filename_nc1 % shiftx=velocity interpolated at position miniy=max(1+isy2+shifty,1+iby2); minix=max(1+isx2-shiftx,1+ibx2); maxiy=min(size(par_civ2.ImageA,1)-isy2+shifty,size(par_civ2.ImageA,1)-iby2); maxix=min(size(par_civ2.ImageA,2)-isx2-shiftx,size(par_civ2.ImageA,2)-ibx2); [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); PointCoord(:,1)=reshape(GridX,[],1); PointCoord(:,2)=reshape(GridY,[],1); if ~isempty(par_civ2.maskname)&& ~strcmp(maskname,par_civ2.maskname)% mask exist, not already read in civ1 mask=imread(par_civ2.maskname); end % caluclate velocity data (y and v in indices, reverse to y component) [xtable ytable utable vtable ctable F] = civ (par_civ2.ImageA,par_civ1.ImageB,ibx2,iby2,isx2,isy2,shiftx,-shifty,PointCoord,str2num(par_civ1.rho),mask); list_param=(fieldnames(par_civ1))'; list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'}; index=zeros(size(list_param)); for ilist=1:length(list_remove) index=strcmp(list_remove{ilist},list_param); if ~isempty(find(index,1)) list_param(index)=[]; end end for ilist=1:length(list_param) Civ1_param{ilist}=['Civ1_' list_param{ilist}]; eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';']) end if isfield(Data,'Civ1_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile') Data.Civ1_gridname=''; end if isfield(Data,'Civ1_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile') Data.Civ1_maskname=''; end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param {'Civ1_Time','Civ1_Dt'}]; Data.Civ1_Time=str2double(par_civ1.T0); Data.Civ1_Dt=str2double(par_civ1.Dt); Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};% cell array containing the names of the fields to record Data.VarDimName={'nbvec1','nbvec1','nbvec1','nbvec1','nbvec1','nbvec1'}; Data.VarAttribute{1}.Role='coord_x'; Data.VarAttribute{2}.Role='coord_y'; Data.VarAttribute{3}.Role='vector_x'; Data.VarAttribute{4}.Role='vector_y'; Data.VarAttribute{5}.Role='warnflag'; Data.Civ1_X=reshape(xtable,[],1); Data.Civ1_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); Data.Civ1_U=reshape(utable,[],1); Data.Civ1_V=reshape(-vtable,[],1); Data.Civ1_C=reshape(ctable,[],1); Data.Civ1_F=reshape(F,[],1); Data.CivStage=Data.CivStage+1; end %% Fix2 if isfield (Param,'Fix2') ListFixParam=fieldnames(Param.Fix2); for ilist=1:length(ListFixParam) ParamName=ListFixParam{ilist}; ListName=['Fix1_' ParamName]; eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) eval(['Data.' ListName '=Param.Fix2.' ParamName ';']) end if check_civx if ~isfield(Data,'fix2') Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; Data.fix2=1; Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; end Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y); else Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; Data.VarDimName=[Data.VarDimName {'nbvec2'}]; nbvar=length(Data.ListVarName); Data.VarAttribute{nbvar}.Role='errorflag'; Data.Civ2_FF=fix(Param.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V); Data.CivStage=5; end end %% Patch2 if isfield (Param,'Patch2') Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; Data.Patch2_Rho=str2double(Param.Patch2.Rho); Data.Patch2_Threshold=str2double(Param.Patch2.Threshold); Data.Patch2_SubDomain=str2double(Param.Patch2.SubDomain); Data.ListVarName=[Data.ListVarName {'Civ2_U_Diff','Civ2_V_Diff','Civ2_X_SubRange','Civ2_Y_SubRange','Civ2_NbSites','Civ2_X_tps','Civ2_Y_tps','Civ2_U_tps','Civ2_V_tps'}]; Data.VarDimName=[Data.VarDimName {'NbVec2','NbVec2',{'NbSubDomain2','Two'},{'NbSubDomain2','Two'},'NbSubDomain2',... {'NbVec2Sub','NbSubDomain2'},{'NbVec2Sub','NbSubDomain2'},{'Nbtps2','NbSubDomain2'},{'Nbtps2','NbSubDomain2'}}]; nbvar=length(Data.ListVarName); Data.VarAttribute{nbvar-1}.Role='vector_x'; Data.VarAttribute{nbvar}.Role='vector_y'; Data.Civ2_U_Diff=zeros(size(Data.Civ2_X)); Data.Civ2_V_Diff=zeros(size(Data.Civ2_X)); if isfield(Data,'Civ2_FF') ind_good=find(Data.Civ2_FF==0); else ind_good=1:numel(Data.Civ2_X); end [Data.Civ2_X_SubRange,Data.Civ2_Y_SubRange,Data.Civ2_NbSites,FFres,Ures, Vres,Data.Civ2_X_tps,Data.Civ2_Y_tps,Data.Civ2_U_tps,Data.Civ2_V_tps]=... patch(Data.Civ2_X(ind_good)',Data.Civ2_Y(ind_good)',Data.Civ2_U(ind_good)',Data.Civ2_V(ind_good)',Data.Patch2_Rho,Data.Patch2_Threshold,Data.Patch2_SubDomain); Data.Civ2_U_Diff(ind_good)=Data.Civ2_U(ind_good)-Ures; Data.Civ2_V_Diff(ind_good)=Data.Civ2_V(ind_good)-Vres; Data.Civ2_FF(ind_good)=FFres; Data.CivStage=6; end %% write result in a netcdf file if requested if exist('ncfile','var') errormsg=struct2nc(ncfile,Data); end % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ %-------------------------------------------------------------------------- % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) % % OUTPUT: % xtable: set of x coordinates % ytable: set of y coordiantes % utable: set of u displacements (along x) % vtable: set of v displacements (along y) % ctable: max image correlation for each vector % typevector: set of flags, =1 for good, =0 for NaN vectors % %INPUT: % image1:first image (matrix) % image2: second image (matrix) % ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1) % isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1) % shiftx, shifty: shift of the search box (in pixel index, yshift reversed) % step: mesh of the measurement points (in px) % subpixfinder=1 or 2 controls the curve fitting of the image correlation % mask: =[] for no mask % roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[]; function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ) %this funtion performs the DCC PIV analysis. Recent window-deformation %methods perform better and will maybe be implemented in the future. %% prepare grid ibx2=ceil(par_civ.Bx/2); iby2=ceil(par_civ.By/2); isx2=ceil(par_civ.Searchx/2); isy2=ceil(par_civ.Searchy/2); shiftx=par_civ.Shiftx; shifty=-par_civ.Shifty;% sign minus because image j index increases when y decreases if isfield(par_civ,'Grid') if ischar(par_civ.Grid) par_civ.Grid; par_civ.Grid=dlmread(par_civ.Grid); par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) end else% automatic measurement grid ibx2=ceil(par_civ.Bx/2); iby2=ceil(par_civ.By/2); isx2=ceil(par_civ.Searchx/2); isy2=ceil(par_civ.Searchy/2); shiftx=par_civ.Shiftx; shifty=-par_civ.Shifty; miniy=max(1+isy2+shifty,1+iby2); minix=max(1+isx2-shiftx,1+ibx2); maxiy=min(par_civ.ImageHeight-isy2+shifty,par_civ.ImageHeight-iby2); maxix=min(par_civ.ImageWidth-isx2-shiftx,par_civ.ImageWidth-ibx2); [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); par_civ.Grid(:,1)=reshape(GridX,[],1); par_civ.Grid(:,2)=reshape(GridY,[],1); end %% Default output nbvec=size(par_civ.Grid,1); xtable=par_civ.Grid(:,1); ytable=par_civ.Grid(:,2); utable=zeros(nbvec,1); vtable=zeros(nbvec,1); ctable=zeros(nbvec,1); F=zeros(nbvec,1); result_conv=[]; errormsg=''; %% prepare mask if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) if strcmp(par_civ.Mask,'all') return % get the grid only, no civ calculation elseif ischar(par_civ.Mask) par_civ.Mask=imread(par_civ.Mask); end end check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); %% prepare images if ischar(par_civ.ImageA) par_civ.ImageA=imread(par_civ.ImageA); end if ischar(par_civ.ImageB) par_civ.ImageB=imread(par_civ.ImageB); end [npy_ima npx_ima]=size(par_civ.ImageA); if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) errormsg='image pair with unequal size'; return end par_civ.ImageA=double(par_civ.ImageA); par_civ.ImageB=double(par_civ.ImageB); %% Apply mask % Convention for mask % mask >200 : velocity calculated % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) % 150>=mask >100: velocity not calculated, nor interpolated % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) TO IMPLEMENT % 20>=mask: velocity=0 checkmask=0; if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) checkmask=1; if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) errormsg='mask must be an image with the same size as the images'; return end % check_noflux=(par_civ.Mask<100) ;%TODO: to implement check_undefined=(par_civ.Mask<200 & par_civ.Mask>=100 ); par_civ.ImageA(check_undefined)=min(min(par_civ.ImageA));% put image A to zero (i.e. the min image value) in the undefined area par_civ.ImageB(check_undefined)=min(min(par_civ.ImageB));% put image B to zero (i.e. the min image value) in the undefined area end %% compute image correlations: MAINLOOP on velocity vectors % corrmax=0; % sum_square=1;% default % vector=[0 0];%default for ivec=1:nbvec iref=par_civ.Grid(ivec,1);% xindex on the image A for the middle of the correlation box jref=par_civ.Grid(ivec,2);% yindex on the image B for the middle of the correlation box % xtable(ivec)=iref; % ytable(ivec)=jref;%default if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth F(ivec)=3; else image1_crop=par_civ.ImageA(jref-iby2:jref+iby2,iref-ibx2:iref+ibx2);%extract a subimage (correlation box) from image A image2_crop=par_civ.ImageB(jref+shifty-isy2:jref+shifty+isy2,iref+shiftx-isx2:iref+shiftx+isx2);%extract a larger subimage (search box) from image B image1_mean=mean(mean(image1_crop)); image2_mean=mean(mean(image2_crop)); %threshold on image minimum if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) F(ivec)=3; end end %threshold on image maximum if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) F(ivec)=3; end if F(ivec)~=3 image1_crop=image1_crop-image1_mean;%substract the mean image2_crop=image2_crop-image2_mean; sum_square=sum(sum(image1_crop.*image1_crop)); %reference: Oliver Pust, PIV: Direct Cross-Correlation result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); corrmax= max(max(result_conv)); result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 %Find the correlation max, at 255 [y,x] = find(result_conv==255,1); if ~isempty(y) && ~isempty(x) try if par_civ.Rho==1 [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); elseif par_civ.Rho==2 [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); end utable(ivec)=vector(1)+shiftx; vtable(ivec)=vector(2)+shifty; xtable(ivec)=iref+utable(ivec)/2;% convec flow (velocity taken at the point middle from imgae1 and 2) ytable(ivec)=jref+vtable(ivec)/2; iref=round(xtable(ivec));% image index for the middle of the vector jref=round(ytable(ivec)); if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100 utable(ivec)=0; vtable(ivec)=0; F(ivec)=3; end ctable(ivec)=corrmax/sum_square;% correlation value catch ME % vector=[0 0]; %if something goes wrong with cross correlation..... F(ivec)=3; end else F(ivec)=3; end end end %Create the vector matrix x, y, u, v end result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output %------------------------------------------------------------------------ % --- Find the maximum of the correlation function after interpolation function [vector,F] = SUBPIXGAUSS (result_conv,x,y) %------------------------------------------------------------------------ vector=[0 0]; %default F=0; [npy,npx]=size(result_conv); % if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1) %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion – Israel Institute of Technology %http://urapiv.wordpress.com peaky = y; if y <= npy-1 && y >= 1 f0 = log(result_conv(y,x)); f1 = real(log(result_conv(y-1,x))); f2 = real(log(result_conv(y+1,x))); peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); else F=-2; % warning flag for vector truncated by the limited search box end peakx=x; if x <= npx-1 && x >= 1 f0 = log(result_conv(y,x)); f1 = real(log(result_conv(y,x-1))); f2 = real(log(result_conv(y,x+1))); peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); else F=-2; % warning flag for vector truncated by the limited search box end vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; %------------------------------------------------------------------------ % --- Find the maximum of the correlation function after interpolation function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) %------------------------------------------------------------------------ vector=[0 0]; %default F=-2; peaky=y; peakx=x; [npy,npx]=size(result_conv); if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) F=0; for i=-1:1 for j=-1:1 %following 15 lines based on %H. Nobach Æ M. Honkanen (2005) %Two-dimensional Gaussian regression for sub-pixel displacement %estimation in particle image velocimetry or particle position %estimation in particle tracking velocimetry %Experiments in Fluids (2005) 38: 511–515 c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); end end c10=(1/6)*sum(sum(c10)); c01=(1/6)*sum(sum(c01)); c11=(1/4)*sum(sum(c11)); c20=(1/6)*sum(sum(c20)); c02=(1/6)*sum(sum(c02)); deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); if abs(deltax)<1 peakx=x+deltax; end if abs(deltay)<1 peaky=y+deltay; end end vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; %'RUN_FIX': function for fixing velocity fields: %----------------------------------------------- % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) % %filename: name of the netcdf file (used as input and output) %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) %.vel_type='civ1' or 'civ2'; %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) %flagindex: flag specifying which values of vec_f are removed: % if flagindex(1)=1: vec_f=-2 vectors are removed % if flagindex(2)=1: vec_f=3 vectors are removed % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) %iter=1 for civ1 fields and iter=2 for civ2 fields %thresh_vecC: threshold in the image correlation vec_C %flag_mask: =1 mask used to remove vectors (0 else) %maskname: name of the mask image file for fix %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold %fileref: .nc file name for a reference velocity (='': refrence 0 used) %fieldref: 'civ1','filter1'...feld used in fileref function FF=fix(Param,F,C,U,V,X,Y) FF=zeros(size(F));%default Param %criterium on warn flags FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; FlagVal=[-2 2 3 4]; for iflag=1:numel(FlagName) if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) FF=(FF==1| F==FlagVal(iflag)); % if isfield (Param,'WarnFlags') % for iflag=1:numel(Param.WarnFlags) % FF=(FF==1| F==Param.WarnFlags(iflag)); % end % end end end %criterium on correlation values if isfield (Param,'MinCorr') FF=FF==1 | C(Param.MaxVel*Param.MaxVel); end end return % % if isfield (Param,'LowerBoundVel')&& ~isequal(Param.LowerBoundVel,0) % thresh=Param.LowerBoundVel*Param.LowerBoundVel; % FF=FF==1 | (U.*U+V.*V)thresh; % end % if isfield(Param,'MaskName') % M=imread(Param.MaskName); % nxy=size(M); % M=reshape(M,1,[]); % rangx0=[0.5 nxy(2)-0.5]; % rangy0=[0.5 nxy(1)-0.5]; % vec_x1=X-U/2;%beginning points % vec_x2=X+U/2;%end points of vectors % vec_y1=Y-V/2;%beginning points % vec_y2=Y+V/2;%end points of vectors % indx=1+round((nxy(2)-1)*(vec_x1-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa vec_x1 % indy=1+round((nxy(1)-1)*(vec_y1-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y1 % check_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside % indx=indx.*check_in+(1-check_in); %replace indx by 1 out of the mask range % indy=indy.*check_in+(1-check_in); %replace indy by 1 out of the mask range % ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector % Mvalues=M(ICOMB); % flag7b=((20 < Mvalues) & (Mvalues < 200))| ~check_in'; % indx=1+round((nxy(2)-1)*(vec_x2-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa vec_x2 % indy=1+round((nxy(1)-1)*(vec_y2-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y2 % check_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside % indx=indx.*check_in+(1-check_in); %replace indx by 1 out of the mask range % indy=indy.*check_in+(1-check_in); %replace indy by 1 out of the mask range % ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector % Mvalues=M(ICOMB); % flag7e=((Mvalues > 20) & (Mvalues < 200))| ~check_in'; % FF=FF==1 |(flag7b|flag7e)'; % end % % flag7=0; % % end % FF=double(FF); % % % criterium on velocity values % delta_u=Field.U;%default without ref file % delta_v=Field.V; % if exist('fileref','var') && ~isempty(fileref) % if ~exist(fileref,'file') % error='reference file not found in RUN_FIX.m'; % display(error); % return % end % FieldRef=read_civxdata(fileref,[],fieldref); % if isfield(FieldRef,'FF') % index_true=find(FieldRef.FF==0); % FieldRef.X=FieldRef.X(index_true); % FieldRef.Y=FieldRef.Y(index_true); % FieldRef.U=FieldRef.U(index_true); % FieldRef.V=FieldRef.V(index_true); % end % if ~isfield(FieldRef,'X') || ~isfield(FieldRef,'Y') || ~isfield(FieldRef,'U') || ~isfield(FieldRef,'V') % error='reference file is not a velocity field in RUN_FIX.m '; %bad input file % return % end % if length(FieldRef.X)<=1 % errordlg('reference field with one vector or less in RUN_FIX.m') % return % end % vec_U_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.U,Field.X,Field.Y); %interpolate vectors in the ref field % vec_V_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.V,Field.X,Field.Y); %interpolate vectors in the ref field to the positions of the main field % delta_u=Field.U-vec_U_ref;%take the difference with the interpolated ref field % delta_v=Field.V-vec_V_ref; % end % thresh_vel_x=thresh_vel; % thresh_vel_y=thresh_vel; % if isequal(inf_sup,1) % flag5=abs(delta_u)thresh_vel_x | abs(delta_v)>thresh_vel_y) &(flag1~=1)&(flag2~=1)&(flag3~=1)&(flag4~=1); % end % % % flag7 introduce a grey mask, matrix M % flagmagenta=flag1|flag2|flag3|flag4|flag5|flag7; % fixflag_unit=Field.FF-10*floor(Field.FF/10); %unity term of fix_flag %------------------------------------------------------------------------ % patch function function [SubRangx,SubRangy,nbpoints,FF,U_smooth,V_smooth,X_tps,Y_tps,U_tps,V_tps] =patch(X,Y,U,V,Rho,Threshold,SubDomain) %subdomain decomposition warning off U=reshape(U,[],1); V=reshape(V,[],1); X=reshape(X,[],1); Y=reshape(Y,[],1); nbvec=numel(X); NbSubDomain=ceil(nbvec/SubDomain); MinX=min(X); MinY=min(Y); MaxX=max(X); MaxY=max(Y); RangX=MaxX-MinX; RangY=MaxY-MinY; AspectRatio=RangY/RangX; NbSubDomainX=max(floor(sqrt(NbSubDomain/AspectRatio)),1); NbSubDomainY=max(floor(sqrt(NbSubDomain*AspectRatio)),1); NbSubDomain=NbSubDomainX*NbSubDomainY; SizX=RangX/NbSubDomainX;%width of subdomains SizY=RangY/NbSubDomainY;%height of subdomains CentreX=linspace(MinX+SizX/2,MaxX-SizX/2,NbSubDomainX); CentreY=linspace(MinY+SizY/2,MaxY-SizY/2,NbSubDomainY); [CentreX,CentreY]=meshgrid(CentreX,CentreY); CentreY=reshape(CentreY,1,[]); CentreX=reshape(CentreX,1,[]); rho=SizX*SizY*Rho/1000000;%optimum rho increase as the area of the subdomain (division by 10^6 to reach good values with the default GUI input) U_tps_sub=zeros(length(X),NbSubDomain);%default spline V_tps_sub=zeros(length(X),NbSubDomain);%default spline U_smooth=zeros(length(X),1); V_smooth=zeros(length(X),1); nb_select=zeros(length(X),1); FF=zeros(length(X),1); check_empty=zeros(1,NbSubDomain); for isub=1:NbSubDomain SubRangx(isub,:)=[CentreX(isub)-SizX/2 CentreX(isub)+SizX/2]; SubRangy(isub,:)=[CentreY(isub)-SizY/2 CentreY(isub)+SizY/2]; ind_sel_previous=[]; ind_sel=0; while numel(ind_sel)>numel(ind_sel_previous) %increase the subdomain during four iterations at most ind_sel_previous=ind_sel; ind_sel=find(X>SubRangx(isub,1) & XSubRangy(isub,1) & YThreshold);%put FF value to 20 to identify the criterium of elimmination ind_ind_sel=find(FF(ind_sel)==0); % select the indices of ind_sel corresponding to the remaining vectors % no value exceeds threshold, the result is recorded if isequal(numel(ind_ind_sel),numel(ind_sel)) U_smooth(ind_sel)=U_smooth(ind_sel)+U_smooth_sub; V_smooth(ind_sel)=V_smooth(ind_sel)+V_smooth_sub; nbpoints(isub)=numel(ind_sel); X_tps(1:nbpoints(isub),isub)=X(ind_sel); Y_tps(1:nbpoints(isub),isub)=Y(ind_sel); U_tps(1:nbpoints(isub)+3,isub)=U_tps_sub; V_tps(1:nbpoints(isub)+3,isub)=V_tps_sub; nb_select(ind_sel)=nb_select(ind_sel)+1; display('good') break % too few selected vectors, increase the subrange for next iteration elseif numel(ind_ind_sel)