%'civ_matlab': main PIV function, calleed by the GUI civ % --- call the sub-functions: % civ: PIV function itself % fix: removes false vectors after detection by various criteria % filter_tps: make interpolation-smoothing %------------------------------------------------------------------------ % function [Data,errormsg,result_conv]= civ_matlab(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 % .Civ1: for civ1 % .Fix1: % .Patch1: % .Civ2: for civ2 % .Fix2: % .Patch2: % 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 % case of input Param set by an xml file (batch mode) if ischar(Param) Param=xml2struct(Param); %if Param is the name of an xml file, read this file as a Matlab structure end %% Civ1 if isfield (Param,'Civ1') par_civ1=Param.Civ1; if isfield(par_civ1,'reverse_pair')% A REVOIR if par_civ1.reverse_pair if ischar(par_civ1.ImageB) temp=par_civ1.ImageA; par_civ1.ImageA=imread(par_civ1.ImageB); end if ischar(temp) par_civ1.ImageB=imread(temp); end end else if isfield(Param.Civ1,'ImageA') && ischar(Param.Civ1.ImageA) Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'''','\'); [par_civ1.ImageA,VideoObject] = read_image(Param.Civ1.ImageA,par_civ1.FileTypeA,[],par_civ1.FrameIndexA); end if isfield(Param.Civ1,'ImageB')&& ischar(Param.Civ1.ImageB) Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'''','\'); if strcmp(Param.Civ1.ImageA,Param.Civ1.ImageB)% use the same movie object [par_civ1.ImageB,VideoObject] = read_image(Param.Civ1.ImageB,par_civ1.FileTypeB,VideoObject,par_civ1.FrameIndexB); else [par_civ1.ImageB,VideoObject] = read_image(Param.Civ1.ImageB,par_civ1.FileTypeB,par_civ1.ImageB,par_civ1.FrameIndexB); end end end list_param=(fieldnames(Param.Civ1))'; Civ1_param=list_param;%default %set the values of all the global attributes in list_param Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param]; for ilist=1:length(list_param) Civ1_param{ilist}=['Civ1_' list_param{ilist}]; Data.(['Civ1_' list_param{ilist}])=Param.Civ1.(list_param{ilist}); end Data.CivStage=1; % set the list of variables Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; 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'; if strcmp(Param.ListCompareMode, 'PIV volume') Data.ListVarName=[Data.ListVarName 'Civ1_Z']; Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[]; for ivol=1:NbSlice % caluclate velocity data (y and v in indices, reverse to y component) [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); if ~isempty(errormsg) return end Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)]; end else %usual PIV % caluclate velocity data (y and v in indices, reverse to y component) [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); if ~isempty(errormsg) return end 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); end else if exist('ncfile','var') CivFile=ncfile; elseif isfield(Param.Patch1,'CivFile') 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; return end if ~isempty(Data.absolut_time_T0')%read civx file check_civx=1;% test for old civx data format [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 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 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 {'nb_vec_1'}]; 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') if check_civx errormsg='Civ Matlab input needed for patch'; return end Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; Data.Patch1_FieldSmooth=Param.Patch1.FieldSmooth; Data.Patch1_MaxDiff=Param.Patch1.MaxDiff; Data.Patch1_SubDomainSize=Param.Patch1.SubDomainSize; nbvar=length(Data.ListVarName); Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',... {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; Data.VarAttribute{nbvar+1}.Role='vector_x'; Data.VarAttribute{nbvar+2}.Role='vector_y'; Data.VarAttribute{nbvar+5}.Role='coord_tps'; Data.VarAttribute{nbvar+6}.Role='vector_x'; Data.VarAttribute{nbvar+7}.Role='vector_y'; Data.Civ1_U_smooth=zeros(size(Data.Civ1_X)); Data.Civ1_V_smooth=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_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomainSize,Data.Patch1_FieldSmooth,Data.Patch1_MaxDiff); Data.Civ1_U_smooth(ind_good)=Ures; Data.Civ1_V_smooth(ind_good)=Vres; Data.Civ1_FF(ind_good)=FFres; Data.CivStage=3; end %% Civ2 if isfield (Param,'Civ2') par_civ2=Param.Civ2; par_civ2.ImageA=[]; par_civ2.ImageB=[]; if isfield(Param.Civ2,'ImageA') && isfield(Param.Civ2,'ImageB') Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'''','\'); Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'''','\'); if isfield (Param,'Civ1') Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'''','\'); if strcmp(Param.Civ1.ImageA,Param.Civ2.ImageA) if isequal(Param.Civ1.FrameIndexA,Param.Civ2.FrameIndexA) par_civ2.ImageA=par_civ1.ImageA; else % read another frame of the same movie object par_civ2.ImageA = read_image(Param.Civ2.ImageA,Param.Civ2.FileTypeA,VideoObject,Param.Civ2.FrameIndexA); end end Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'''','\'); if strcmp(Param.Civ1.ImageB,Param.Civ2.ImageB) if isequal(Param.Civ1.FrameIndexB,Param.Civ2.FrameIndexB) par_civ2.ImageB=par_civ1.ImageB; else % read another frame of the same movie object par_civ2.ImageB = read_image(Param.Civ2.ImageB,Param.Civ2.FileTypeB,VideoObject,Param.Civ2.FrameIndexB); end end end if isempty(par_civ2.ImageA) && isfield(Param.Civ2,'ImageA') [par_civ2.ImageA,VideoObject] = read_image(Param.Civ2.ImageA,Param.Civ2.FileTypeA,[],Param.Civ2.FrameIndexA); end if isempty(par_civ2.ImageB)&& isfield(Param.Civ2,'ImageB') if strcmp(Param.Civ2.ImageA,Param.Civ2.ImageB) par_civ2.ImageB = read_image(Param.Civ2.ImageB,Param.Civ2.FileTypeB,VideoObject,Param.Civ2.FrameIndexB); else par_civ2.ImageB = read_image(Param.Civ2.ImageB,Param.Civ2.FileTypeB,[],Param.Civ2.FrameIndexB); end end end % ibx2=ceil(par_civ2.CorrBoxSize(1)/2); % iby2=ceil(par_civ2.CorrBoxSize(2)/2); % isx2=ibx2+4;% search ara +-4 pixels around the guess % isy2=iby2+4; % % shift from par_civ2.filename_nc1 % % shiftx=velocity interpolated at position % miniy=max(1+isy2,1+iby2); % minix=max(1+isx2,1+ibx2); % maxiy=min(size(par_civ2.ImageA,1)-isy2,size(par_civ2.ImageA,1)-iby2); % maxix=min(size(par_civ2.ImageA,2)-isx2,size(par_civ2.ImageA,2)-ibx2); % [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); % GridX=reshape(GridX,[],1); % GridY=reshape(GridY,[],1); if isfield(par_civ2,'Grid')% grid points set as input file if ischar(par_civ2.Grid)%read the grid file if the input is a file name par_civ2.Grid=dlmread(par_civ2.Grid); par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) end else% automatic grid minix=floor(par_civ2.Dx/2)-0.5; maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); miniy=floor(par_civ2.Dy/2)-0.5; maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); par_civ2.Grid(:,1)=reshape(GridX,[],1); par_civ2.Grid(:,2)=reshape(GridY,[],1); end Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data Shifty=zeros(size(par_civ2.Grid,1),1); nbval=zeros(size(par_civ2.Grid,1),1); if par_civ2.CheckDeformation DUDX=zeros(size(par_civ2.Grid,1),1); DUDY=zeros(size(par_civ2.Grid,1),1); DVDX=zeros(size(par_civ2.Grid,1),1); DVDY=zeros(size(par_civ2.Grid,1),1); end 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 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) EM = tps_eval(epoints,ctrs); Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub); Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub); if par_civ2.CheckDeformation [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub); DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub); DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub); DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub); end end mask=''; if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 mask=imread(par_civ2.Mask); end ibx2=ceil(par_civ2.CorrBoxSize(1)/2); iby2=ceil(par_civ2.CorrBoxSize(2)/2); % isx2=ibx2+4;% search ara +-4 pixels around the guess % isy2=iby2+4; par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess par_civ2.SearchBoxSize(2)=2*iby2+9; %par_civ2.SearchBoxSize(1)=2*isx2+1; %par_civ2.SearchBoxSize(2)=2*isy2+1; 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 if par_civ2.CheckDeformation par_civ2.DUDX=DUDX./nbval; par_civ2.DUDY=DUDY./nbval; par_civ2.DVDX=DVDX./nbval; par_civ2.DVDY=DVDY./nbval; end % caluclate velocity data (y and v in indices, reverse to y component) [xtable ytable utable vtable ctable F] = civ (par_civ2); list_param=(fieldnames(Param.Civ2))'; list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'}; 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) Civ2_param{ilist}=['Civ2_' list_param{ilist}]; eval(['Data.Civ2_' list_param{ilist} '=Param.Civ2.' list_param{ilist} ';']) end if isfield(Data,'Civ2_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile') Data.Civ1_gridname=''; end if isfield(Data,'Civ2_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile') Data.Civ2_maskname=''; end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}]; nbvar=numel(Data.ListVarName); Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];% cell array containing the names of the fields to record Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; Data.VarAttribute{nbvar+1}.Role='coord_x'; Data.VarAttribute{nbvar+2}.Role='coord_y'; Data.VarAttribute{nbvar+3}.Role='vector_x'; Data.VarAttribute{nbvar+4}.Role='vector_y'; Data.VarAttribute{nbvar+5}.Role='warnflag'; Data.Civ2_X=reshape(xtable,[],1); Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); Data.Civ2_U=reshape(utable,[],1); Data.Civ2_V=reshape(-vtable,[],1); Data.Civ2_C=reshape(ctable,[],1); Data.Civ2_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=['Fix2_' 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 {'nb_vec_2'}]; 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=Data.CivStage+1; end end %% Patch2 if isfield (Param,'Patch2') Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; Data.Patch2_FieldSmooth=Param.Patch2.FieldSmooth; Data.Patch2_MaxDiff=Param.Patch2.MaxDiff; Data.Patch2_SubDomainSize=Param.Patch2.SubDomainSize; nbvar=length(Data.ListVarName); Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; Data.VarAttribute{nbvar+1}.Role='vector_x'; Data.VarAttribute{nbvar+2}.Role='vector_y'; Data.VarAttribute{nbvar+5}.Role='coord_tps'; Data.VarAttribute{nbvar+6}.Role='vector_x'; Data.VarAttribute{nbvar+7}.Role='vector_y'; Data.Civ2_U_smooth=zeros(size(Data.Civ2_X)); Data.Civ2_V_smooth=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_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomainSize,Data.Patch2_FieldSmooth,Data.Patch2_MaxDiff); Data.Civ2_U_smooth(ind_good)=Ures; Data.Civ2_V_smooth(ind_good)=Vres; Data.Civ2_FF(ind_good)=FFres; Data.CivStage=Data.CivStage+1; end %% write result in a netcdf file if requested if exist('ncfile','var') errormsg=struct2nc(ncfile,Data); if isempty(errormsg) disp([ncfile ' written']) else disp(errormsg) end 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: % par_civ: structure of input parameters, with fields: % .CorrBoxSize % .SearchBoxSize % .SearchBoxShift % .ImageHeight % .ImageWidth % .Dx, Dy % .Grid % .Mask % .MinIma % .MaxIma % .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 measurement grid if isfield(par_civ,'Grid')% grid points set as input if ischar(par_civ.Grid)%read the drid file if the input is a file name 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 grid minix=floor(par_civ.Dx/2)-0.5; maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); miniy=floor(par_civ.Dy/2)-0.5; maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); [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 nbvec=size(par_civ.Grid,1); %% prepare correlation and search boxes ibx2=ceil(par_civ.CorrBoxSize(1)/2); iby2=ceil(par_civ.CorrBoxSize(2)/2); isx2=ceil(par_civ.SearchBoxSize(1)/2); isy2=ceil(par_civ.SearchBoxSize(2)/2); shiftx=round(par_civ.SearchBoxShift(:,1)); shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases if numel(shiftx)==1% case of a unique shift for the whole field( civ1) shiftx=shiftx*ones(nbvec,1); shifty=shifty*ones(nbvec,1); end %% Default output 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 isfield(par_civ,'reverse_pair') % if par_civ.reverse_pair % if ischar(par_civ.ImageB) % temp=par_civ.ImageA; % par_civ.ImageA=imread(par_civ.ImageB); % end % if ischar(temp) % par_civ.ImageB=imread(temp); % end % end % else % 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 % end par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images par_civ.ImageB=sum(double(par_civ.ImageB),3); [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 %% Apply mask % Convention for mask IDEAS TO IMPLEMENT ? % 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) % 20>=mask: velocity=0 checkmask=0; MinA=min(min(par_civ.ImageA)); MinB=min(min(par_civ.ImageB)); 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>=20 ); par_civ.ImageA(check_undefined)=MinA;% put image A to zero (i.e. the min image value) in the undefined area par_civ.ImageB(check_undefined)=MinB;% 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 mesh=1;% default CheckDecimal=isfield(par_civ,'CheckDecimal')&& par_civ.CheckDecimal==1; if CheckDecimal mesh=0.2;%mesh in pixels for subpixel image interpolation CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; end % vector=[0 0];%default for ivec=1:nbvec iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box %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||... % jref+shifty(ivec)-isy2<1||jref+shifty(ivec)+isy2>par_civ.ImageHeight|| iref+shiftx(ivec)-isx2<1 || iref+shiftx(ivec)+isx2>par_civ.ImageWidth % we are outside the image % F(ivec)=3; % else F(ivec)=0; subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; image1_crop(check1_y,check1_x)=par_civ.ImageA(subrange1_y(check1_y),subrange1_x(check1_x));%extract a subimage (correlation box) from image A image2_crop(check2_y,check2_x)=par_civ.ImageB(subrange2_y(check2_y),subrange2_x(check2_x));%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 %threshold on image maximum if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) F(ivec)=3; end % end if F(ivec)~=3 image1_crop=image1_crop-image1_mean;%substract the mean image2_crop=image2_crop-image2_mean; if CheckDecimal xi=(1:mesh:size(image1_crop,2)); yi=(1:mesh:size(image1_crop,1))'; if CheckDeformation [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); image1_crop=interp2(image1_crop,XIant,YIant); else image1_crop=interp2(image1_crop,xi,yi); end xi=(1:mesh:size(image2_crop,2)); yi=(1:mesh:size(image2_crop,1))'; image2_crop=interp2(image2_crop,xi,yi); end 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.CorrSmooth==1 [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); elseif par_civ.CorrSmooth==2 [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); end utable(ivec)=vector(1)*mesh+shiftx(ivec); vtable(ivec)=vector(2)*mesh+shifty(ivec); xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) 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 F(ivec)=3; end else F(ivec)=3; end end 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 � 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 %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)); end end %criterium on correlation values if isfield (Param,'MinCorr') FF=FF==1 | C(Param.MaxVel*Param.MaxVel); end end