%'stereo_series': PIV function activated by the general GUI series % --- 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_series(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 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France %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]= stereo_civ(Param) Data=[]; errormsg=''; %% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN if size(Param.InputTable,1)<2 msgbox_uvmat('WARNING','two input file series must be entered') return end path_series=fileparts(which('series')); addpath(fullfile(path_series,'series')) Data=stereo_input(Param);% introduce the civ parameters using the GUI stereo_input if isempty(Data) Data=Param;% if civ_input has been cancelled, keep previous parameters end Data.Program=mfilename;%gives the name of the current function Data.AllowInputSort='on';% 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) 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) Data.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) Data.FieldTransform = 'off';%can use a transform function (use it by force, no input option) Data.ProjObject='off';%can use projection object(option 'off'/'on', Data.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) Data.OutputDirExt='.stereo';%set the output dir extension Data.OutputSubDirMode='auto'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default) 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) return end %% read input parameters from an xml file if input is a file name (batch mode) checkrun=1; if ischar(Param) Param=xml2struct(Param);% read Param as input file (batch case) checkrun=0; end if ~isfield(Param,'ActionInput') disp_uvmat('ERROR','no parameter set for PIV',checkrun) return end hseries=findobj(allchild(0),'Tag','series'); RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series %% input files and indexing MaxIndex_i=Param.IndexRange.MaxIndex_i; MinIndex_i=Param.IndexRange.MinIndex_i; if ~isfield(Param,'InputTable') disp_uvmat('ERROR', 'no input field',checkrun) return end [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); time=[]; for iview=1:size(Param.InputTable,1) XmlFileName=find_imadoc(Param.InputTable{iview,1},Param.InputTable{iview,2}); if isempty(XmlFileName) disp_uvmat('ERROR', [XmlFileName ' not found'],checkrun) return end XmlData{iview}=imadoc2struct(XmlFileName); if isfield(XmlData{iview},'Time') time=XmlData{iview}.Time; TimeSource='xml'; end if isfield(XmlData{iview},'Camera') if isfield(XmlData{iview}.Camera,'NbSlice')&& ~isempty(XmlData{iview}.Camera.NbSlice) NbSlice_calib{iview}=XmlData{iview}.Camera.NbSlice;% Nbre of slices for Zindex in phys transform if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); end end if isfield(XmlData{iview}.Camera,'TimeUnit')&& ~isempty(XmlData{iview}.Camera.TimeUnit) TimeUnit=XmlData{iview}.Camera.TimeUnit; end end end iview_A=1;% series index (iview) for the first image series iview_B=2;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) RootPath_A=Param.InputTable{1,1}; RootFile_A=Param.InputTable{1,3}; SubDir_A=Param.InputTable{1,2}; NomType_A=Param.InputTable{1,4}; FileExt_A=Param.InputTable{1,5}; RootPath_B=Param.InputTable{2,1}; RootFile_B=Param.InputTable{2,3}; SubDir_B=Param.InputTable{2,2}; NomType_B=Param.InputTable{2,4}; FileExt_B=Param.InputTable{2,5}; PairCiv2=''; i1_series_Civ1=i1_series{1};i1_series_Civ2=i1_series{1}; i2_series_Civ1=i1_series{2};i2_series_Civ2=i1_series{2}; if isempty(j1_series{1}) FrameIndex_A_Civ1=i1_series_Civ1; FrameIndex_B_Civ1=i2_series_Civ1; j1_series_Civ1=ones(size(i1_series{1})); j2_series_Civ1=ones(size(i1_series{2})); else j1_series_Civ1=j1_series{1}; j2_series_Civ1=j1_series{2}; FrameIndex_A_Civ1=j1_series_Civ1; FrameIndex_B_Civ1=j2_series_Civ1; end j1_series_Civ2=j1_series_Civ1; j2_series_Civ2=j2_series_Civ1; if isempty(PairCiv2) FrameIndex_A_Civ2=FrameIndex_A_Civ1; FrameIndex_B_Civ2=FrameIndex_B_Civ1; else if isempty(j1_series_Civ2) FrameIndex_A_Civ2=i1_series_Civ2; FrameIndex_B_Civ2=i2_series_Civ2; j1_series_Civ2=ones(size(i1_series_Civ2)); j2_series_Civ2=ones(size(i1_series_Civ2)); else FrameIndex_A_Civ2=j1_series_Civ2; FrameIndex_B_Civ2=j2_series_Civ2; end end if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) return end %% check the first image pair try if Param.ActionInput.CheckCiv1% Civ1 is performed ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1)); if ~exist(ImageName_A,'file') disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) return end [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); FileType_A=FileInfo_A.FileType; if strcmp(FileInfo_A.FileType,'netcdf') FieldName_A=Param.InputFields.FieldName; [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); par_civ1.ImageA=DataIn.(FieldName_A); else [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1)); end ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1),[],j2_series_Civ1(1)); if ~exist(ImageName_B,'file') disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) return end [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); FileType_B=FileInfo_B.FileType; if strcmp(FileInfo_B.FileType,'netcdf') FieldName_B=Param.InputFields.FieldName; [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); par_civ1.ImageB=DataIn.(FieldName_B); else [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1)); end NbField=numel(i1_series_Civ1); elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ2(1),[],j1_series_Civ2(1)); if ~exist(ImageName_A,'file') disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) return end [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); FileType_A=FileInfo_A.FileType; [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileInfo_A.FileType,VideoObject_A,FrameIndex_A_Civ2(1)); ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(1),[],j2_series_Civ2(1)); if ~exist(ImageName_B,'file') disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) return end [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); FileType_B=FileInfo_B.FileType; [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1)); NbField=numel(i1_series_Civ2); else NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK end catch ME if ~isempty(ME.message) disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) return end end if ismember(FileType_A,{'mmreader','video','cine_phantom'}) NomTypeNc='_1'; else NomTypeNc=NomType_A; end %% Output directory OutputDir=[Param.OutputSubDir Param.OutputDirExt]; ListGlobalAttribute={'Conventions','Program','CivStage'}; Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes Data.Program=mfilename;%gives the name of the current function; Data.CivStage=0;%default maskname='';%default check_civx=0;%default %% get timing from input video if isempty(time) && ismember(FileType_A,{'mmreader','video','cine_phantom'})% case of video input 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(time)% time = index i by default MaxIndex_i=max(i2_series_Civ1); MaxIndex_j=max(j2_series_Civ1); time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); time=[zeros(1,MaxIndex_j);time];% insert a first line of zeros time=[zeros(MaxIndex_i+1,1) time];% insert a first column of zeros end if length(FileInfo_A) >1 %case of image with multiple frames nbfield=length(FileInfo_A); nbfield_j=1; end tic %%%%% MAIN LOOP %%%%%% CheckOverwrite=1;%default if isfield(Param,'CheckOverwrite') CheckOverwrite=Param.CheckOverwrite; end for ifield=1:NbField update_waitbar(WaitbarHandle,ifield/NbField) if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') break end % variable for light saving or not. LSM=Param.ActionInput.CheckLSM; Civ1Dir=OutputDir; ncfile2=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... j1_series_Civ1(ifield),j2_series_Civ1(ifield)); if (~CheckOverwrite && exist(ncfile,'file')) || (~CheckOverwrite && exist(ncfile2,'file')) disp('existing output file already exists, skip to next field') result_conv=0; continue% skip iteration if the mode overwrite is desactivated and the result file already exists end %% Civ1 % if Civ1 computation is requested if isfield (Param.ActionInput,'Civ1') par_civ1=Param.ActionInput.Civ1; try ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); [A{1},VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); [A{2},VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); catch ME if ~isempty(ME.message) disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) return end end [A,Rangx,Rangy]=phys_ima(A,XmlData,1); [Npy,Npx]=size(A{1}); PhysImageA=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.png','_1a',i1_series_Civ1(ifield),[],1); PhysImageB=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.png','_1a',i1_series_Civ1(ifield),[],2); if LSM ~= 1 imwrite(A{1},PhysImageA) imwrite(A{2},PhysImageB) end par_civ1.ImageA=A{1}; par_civ1.ImageB=A{2}; par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width; par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height; list_param=(fieldnames(Param.ActionInput.Civ1))'; Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images %indicate the values of all the global attributes in the output data Data.Civ1_ImageA=ImageName_A; Data.Civ1_ImageB=ImageName_B; i1=i1_series_Civ1(ifield); i2=i1; if ~isempty(i2_series_Civ1) i2=i2_series_Civ1(ifield); end j1=1; if ~isempty(j1_series_Civ1) j1=j1_series_Civ1(ifield); end j2=j1; if ~isempty(j2_series_Civ1) j2=j2_series_Civ1(ifield); end Data.Civ1_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); for ilist=1:length(list_param) Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); end Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; 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'; % calculate velocity data (y and v in indices, reverse to y component) [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); Data.Civ1_X=reshape(xtable,[],1); Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1); % get z from u and v (displacements) 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 %% Fix1 if isfield (Param.ActionInput,'Fix1') if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1 Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute)); Data.ListGlobalAttribute(Fix1_attr)=[]; for ilist=1:numel(Fix1_attr) Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)}); end end ListFixParam=fieldnames(Param.ActionInput.Fix1); for ilist=1:length(ListFixParam) ParamName=ListFixParam{ilist}; ListName=['Fix1_' ParamName]; eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) eval(['Data.' ListName '=Param.ActionInput.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.ActionInput.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.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); Data.CivStage=2; end end %% Patch1 if isfield (Param.ActionInput,'Patch1') if check_civx errormsg='Civ Matlab input needed for patch'; disp_uvmat('ERROR',errormsg,checkrun) return end Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; Data.Patch1_FieldSmooth=Param.ActionInput.Patch1.FieldSmooth; Data.Patch1_MaxDiff=Param.ActionInput.Patch1.MaxDiff; Data.Patch1_SubDomainSize=Param.ActionInput.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.ActionInput,'Civ2') par_civ2=Param.ActionInput.Civ2; par_civ2.ImageA=par_civ1.ImageA; par_civ2.ImageB=par_civ1.ImageB; % if ~isfield(Param.Civ1,'ImageA') i1=i1_series_Civ2(ifield); i2=i1; if ~isempty(i2_series_Civ2) i2=i2_series_Civ2(ifield); end j1=1; if ~isempty(j1_series_Civ2) j1=j1_series_Civ2(ifield); end j2=j1; if ~isempty(j2_series_Civ2) j2=j2_series_Civ2(ifield); end par_civ2.ImageWidth=size(par_civ2.ImageA,2); par_civ2.ImageHeight=size(par_civ2.ImageA,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% 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) 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 par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; 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>=1)./nbval(nbval>=1); par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1); par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1); par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1); end % calculate velocity data (y and v in indices, reverse to y component) [xtable, ytable, utable, vtable, ctable, F] = civ (par_civ2); list_param=(fieldnames(Param.ActionInput.Civ2))'; Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before each string in list_param Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images %indicate the values of all the global attributes in the output data Data.Civ2_ImageA=ImageName_A; Data.Civ2_ImageB=ImageName_B; Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; Data.Civ2_Dt=0; for ilist=1:length(list_param) Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; 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.ActionInput,'Fix2') ListFixParam=fieldnames(Param.ActionInput.Fix2); for ilist=1:length(ListFixParam) ParamName=ListFixParam{ilist}; ListName=['Fix2_' ParamName]; eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) eval(['Data.' ListName '=Param.ActionInput.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=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V)); Data.CivStage=Data.CivStage+1; end end %% Patch2 if isfield (Param.ActionInput,'Patch2') Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; Data.Patch2_FieldSmooth=Param.ActionInput.Patch2.FieldSmooth; Data.Patch2_MaxDiff=Param.ActionInput.Patch2.MaxDiff; Data.Patch2_SubDomainSize=Param.ActionInput.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 %% Civ3 if isfield (Param.ActionInput,'Civ3') par_civ3=Param.ActionInput.Civ3; par_civ3.ImageA=par_civ1.ImageA; par_civ3.ImageB=par_civ1.ImageB; par_civ3.ImageWidth=size(par_civ3.ImageA,2); par_civ3.ImageHeight=size(par_civ3.ImageA,1); if isfield(par_civ3,'Grid')% grid points set as input file if ischar(par_civ3.Grid)%read the grid file if the input is a file name par_civ3.Grid=dlmread(par_civ3.Grid); par_civ3.Grid(1,:)=[];%the first line must be removed (heading in the grid file) end else% automatic grid minix=floor(par_civ3.Dx/2)-0.5; maxix=minix+par_civ3.Dx*floor((par_civ3.ImageWidth-1)/par_civ3.Dx); miniy=floor(par_civ3.Dy/2)-0.5; maxiy=minix+par_civ3.Dy*floor((par_civ3.ImageHeight-1)/par_civ3.Dy); [GridX,GridY]=meshgrid(minix:par_civ3.Dx:maxix,miniy:par_civ3.Dy:maxiy); par_civ3.Grid(:,1)=reshape(GridX,[],1); par_civ3.Grid(:,2)=reshape(GridY,[],1); end Shiftx=zeros(size(par_civ3.Grid,1),1);% shift expected from civ2 data Shifty=zeros(size(par_civ3.Grid,1),1); nbval=zeros(size(par_civ3.Grid,1),1); if par_civ3.CheckDeformation DUDX=zeros(size(par_civ3.Grid,1),1); DUDY=zeros(size(par_civ3.Grid,1),1); DVDX=zeros(size(par_civ3.Grid,1),1); DVDY=zeros(size(par_civ3.Grid,1),1); end NbSubDomain=size(Data.Civ2_SubRange,3); % get the guess from patch2 for isub=1:NbSubDomain% for each sub-domain of Patch2 nbvec_sub=Data.Civ2_NbCentres(isub);% nbre of Civ2 vectors in the subdomain ind_sel=find(par_civ3.Grid(:,1)>=Data.Civ2_SubRange(1,1,isub) & par_civ3.Grid(:,1)<=Data.Civ2_SubRange(1,2,isub) &... par_civ3.Grid(:,2)>=Data.Civ2_SubRange(2,1,isub) & par_civ3.Grid(:,2)<=Data.Civ2_SubRange(2,2,isub)); epoints = par_civ3.Grid(ind_sel,:);% coordinates of interpolation sites ctrs=Data.Civ2_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.Civ2_U_tps(1:nbvec_sub+3,isub); Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ2_V_tps(1:nbvec_sub+3,isub); if par_civ3.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.Civ2_U_tps(1:nbvec_sub+3,isub); DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ2_U_tps(1:nbvec_sub+3,isub); DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ2_V_tps(1:nbvec_sub+3,isub); DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ2_V_tps(1:nbvec_sub+3,isub); end end mask=''; if par_civ3.CheckMask&&~isempty(par_civ3.Mask)&& ~strcmp(maskname,par_civ3.Mask)% mask exist, not already read in Civ2 mask=imread(par_civ3.Mask); end par_civ3.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; par_civ3.Grid=[par_civ3.Grid(nbval>=1,1)-par_civ3.SearchBoxShift(:,1)/2 par_civ3.Grid(nbval>=1,2)-par_civ3.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors if par_civ3.CheckDeformation par_civ3.DUDX=DUDX(nbval>=1)./nbval(nbval>=1); par_civ3.DUDY=DUDY(nbval>=1)./nbval(nbval>=1); par_civ3.DVDX=DVDX(nbval>=1)./nbval(nbval>=1); par_civ3.DVDY=DVDY(nbval>=1)./nbval(nbval>=1); end % calculate velocity data (y and v in indices, reverse to y component) [xtable, ytable, utable, vtable, ctable, F] = civ (par_civ3); list_param=(fieldnames(Param.ActionInput.Civ3))'; Civ3_param=regexprep(list_param,'^.+','Civ3_$0');% insert 'Civ3_' before each string in list_param Civ3_param=[{'Civ3_ImageA','Civ3_ImageB','Civ3_Time','Civ3_Dt'} Civ3_param]; %insert the names of the two input images %indicate the values of all the global attributes in the output data Data.Civ3_ImageA=ImageName_A; Data.Civ3_ImageB=ImageName_B; Data.Civ3_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; Data.Civ3_Dt=0; for ilist=1:length(list_param) Data.(Civ3_param{4+ilist})=Param.ActionInput.Civ3.(list_param{ilist}); end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ3_param]; nbvar=numel(Data.ListVarName); Data.ListVarName=[Data.ListVarName {'Civ3_X','Civ3_Y','Civ3_U','Civ3_V','Civ3_F','Civ3_C','Xphys','Yphys','Zphys'}];% cell array containing the names of the fields to record Data.VarDimName=[Data.VarDimName {'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}]; 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.Civ3_X=reshape(xtable,[],1); Data.Civ3_Y=reshape(size(par_civ3.ImageA,1)-ytable+1,[],1); Data.Civ3_U=reshape(utable,[],1); Data.Civ3_V=reshape(-vtable,[],1); Data.Civ3_C=reshape(ctable,[],1); Data.Civ3_F=reshape(F,[],1); Data.CivStage=Data.CivStage+1; end %% Fix3 if isfield (Param.ActionInput,'Fix3') ListFixParam=fieldnames(Param.ActionInput.Fix3); for ilist=1:length(ListFixParam) ParamName=ListFixParam{ilist}; ListName=['Fix3_' ParamName]; eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) eval(['Data.' ListName '=Param.ActionInput.Fix3.' ParamName ';']) end if check_civx if ~isfield(Data,'fix3') Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix3']; Data.fix3=1; Data.ListVarName=[Data.ListVarName {'vec3_FixFlag'}]; Data.VarDimName=[Data.VarDimName {'nb_vectors3'}]; end Data.vec_FixFlag=fix(Param.Fix3,Data.vec3_F,Data.vec3_C,Data.vec3_U,Data.vec3_V,Data.vec3_X,Data.vec3_Y); else Data.ListVarName=[Data.ListVarName {'Civ3_FF'}]; Data.VarDimName=[Data.VarDimName {'nb_vec_3'}]; nbvar=length(Data.ListVarName); Data.VarAttribute{nbvar}.Role='errorflag'; Data.Civ3_FF=double(fix(Param.ActionInput.Fix3,Data.Civ3_F,Data.Civ3_C,Data.Civ3_U,Data.Civ3_V)); Data.CivStage=Data.CivStage+1; end end %% Patch3 if isfield (Param.ActionInput,'Patch3') Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch3_Rho','Patch3_Threshold','Patch3_SubDomain'}]; Data.Patch3_FieldSmooth=Param.ActionInput.Patch3.FieldSmooth; Data.Patch3_MaxDiff=Param.ActionInput.Patch3.MaxDiff; Data.Patch3_SubDomainSize=Param.ActionInput.Patch3.SubDomainSize; nbvar=length(Data.ListVarName); Data.ListVarName=[Data.ListVarName {'Civ3_U_smooth','Civ3_V_smooth','Civ3_SubRange','Civ3_NbCentres','Civ3_Coord_tps','Civ3_U_tps','Civ3_V_tps','Xmid','Ymid','Uphys','Vphys','Error'}]; Data.VarDimName=[Data.VarDimName {'nb_vec_3','nb_vec_3',{'nb_coord','nb_bounds','nb_subdomain_3'},{'nb_subdomain_3'},... {'nb_tps_3','nb_coord','nb_subdomain_3'},{'nb_tps_3','nb_subdomain_3'},{'nb_tps_3','nb_subdomain_3'},'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}]; 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.Civ3_U_smooth=zeros(size(Data.Civ3_X)); Data.Civ3_V_smooth=zeros(size(Data.Civ3_X)); if isfield(Data,'Civ3_FF') ind_good=find(Data.Civ3_FF==0); else ind_good=1:numel(Data.Civ3_X); end [Data.Civ3_SubRange,Data.Civ3_NbCentres,Data.Civ3_Coord_tps,Data.Civ3_U_tps,Data.Civ3_V_tps,tild,Ures, Vres,tild,FFres]=... filter_tps([Data.Civ3_X(ind_good) Data.Civ3_Y(ind_good)],Data.Civ3_U(ind_good),Data.Civ3_V(ind_good),[],Data.Patch3_SubDomainSize,Data.Patch3_FieldSmooth,Data.Patch3_MaxDiff); Data.Civ3_U_smooth(ind_good)=Ures; Data.Civ3_V_smooth(ind_good)=Vres; Data.Civ3_FF(ind_good)=FFres; Data.CivStage=Data.CivStage+1; % get z from u and v (displacements) Data.Xmid=Rangx(1)+(Rangx(2)-Rangx(1))*(Data.Civ3_X-0.5)/(Npx-1);%temporary coordinate (velocity taken at the point middle from imgae 1 and 2) Data.Ymid=Rangy(2)+(Rangy(1)-Rangy(2))*(Data.Civ3_Y-0.5)/(Npy-1);%temporary coordinate (velocity taken at the point middle from imgae 1 and 2) Data.Uphys=Data.Civ3_U_smooth*(Rangx(2)-Rangx(1))/(Npx-1); Data.Vphys=Data.Civ3_V_smooth*(Rangy(1)-Rangy(2))/(Npy-1); [Data.Zphys,Data.Xphys,Data.Yphys,Data.Error]=shift2z(Data.Xmid,Data.Ymid,Data.Uphys,Data.Vphys,XmlData); %Data.Xphys and Data.Xphys are real coordinate (geometric correction more accurate than xtemp/ytemp) if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) return end end %% write result in a netcdf file if requested if LSM ~= 1 % store all data if exist('ncfile','var') errormsg=struct2nc(ncfile,Data); if isempty(errormsg) disp([ncfile ' written']) else disp(errormsg) end end else % store only phys data Data_light.ListVarName={'Xphys','Yphys','Zphys','Civ3_C','DX','DY','Error'}; Data_light.VarDimName={'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}; Data_light.VarAttribute{1}.Role='coord_x'; Data_light.VarAttribute{2}.Role='coord_y'; Data_light.VarAttribute{3}.Role='scalar'; Data_light.VarAttribute{5}.Role='vector_x'; Data_light.VarAttribute{6}.Role='vector_y'; ind_good=find(Data.Civ3_FF==0); Data_light.Zphys=Data.Zphys(ind_good); Data_light.Yphys=Data.Yphys(ind_good); Data_light.Xphys=Data.Xphys(ind_good); Data_light.Civ3_C=Data.Civ3_C(ind_good); Data_light.DX=Data.Uphys(ind_good); Data_light.DY=Data.Vphys(ind_good); Data_light.Error=Data.Error(ind_good); if exist('ncfile2','var') errormsg=struct2nc(ncfile2,Data_light); if isempty(errormsg) disp([ncfile2 ' written']) else disp(errormsg) end end end end disp(['ellapsed time for the loop ' num2str(toc) ' s']) tic while toc < rand(1)*10 for i = 1:100000, sqrt(1237); 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=floor(par_civ.CorrBoxSize(1)/2); iby2=floor(par_civ.CorrBoxSize(2)/2); isx2=floor(par_civ.SearchBoxSize(1)/2); isy2=floor(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); 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)); %check_undefined=false(size(par_civ.ImageA)); 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 CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; if CheckDeformation mesh=0.25;%mesh in pixels for subpixel image interpolation 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 mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask 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 if checkmask mask1_crop(check1_y,check1_x)=check_undefined(subrange1_y(check1_y),subrange1_x(check1_x));%extract a mask subimage (correlation box) from image A mask2_crop(check2_y,check2_x)=check_undefined(subrange2_y(check2_y),subrange2_x(check2_x));%extract a mask subimage (search box) from imag sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image if sizemask > 1/2% eliminate point if more than half of the correlation box is masked F(ivec)=3; % else image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1) image2_crop=image2_crop.*~mask2_crop; image1_mean=mean(mean(image1_crop))/(1-sizemask); image2_mean=mean(mean(image2_crop))/(1-sizemask); end else image1_mean=mean(mean(image1_crop)); image2_mean=mean(mean(image2_crop)); end %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 if F(ivec)~=3 image1_crop=(image1_crop-image1_mean);%substract the mean, put to zero the masked parts image2_crop=(image2_crop-image2_mean); if checkmask image1_crop=image1_crop.*~mask1_crop;% put to zero the masked parts image2_crop=image2_crop.*~mask2_crop; end if CheckDeformation xi=(1:mesh:size(image1_crop,2)); yi=(1:mesh:size(image1_crop,1))'; [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); image1_crop(isnan(image1_crop))=0; xi=(1:mesh:size(image2_crop,2)); yi=(1:mesh:size(image2_crop,1))'; image2_crop=interp2(image2_crop,xi,yi,'*spline'); image2_crop(isnan(image2_crop))=0; end sum_square=(sum(sum(image1_crop.*image1_crop)));%+sum(sum(image2_crop.*image2_crop)))/2; %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); subimage2_crop=image2_crop(y:y+2*iby2/mesh,x:x+2*ibx2/mesh);%subimage of image 2 corresponding to the optimum displacement of first image sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2 sum_square=sqrt(sum_square);% sqrt of the variance product to normalise correlation 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); result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) %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 = log(result_conv(y-1,x)); f2 = 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 = log(result_conv(y,x-1)); f2 = 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; result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) [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 %------------------------------------------------------------------------ % --- determine the list of index pairs of processing file function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=... find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) %------------------------------------------------------------------------ i1_series=i_series;% set of first image indexes i2_series=i_series; j1_series=j_series;%ones(size(i_series));% set of first image numbers j2_series=j_series;%ones(size(i_series)); r=regexp(str_civ,'^\D(?[i|j])=( -| )(?\d+)\|(?\d+)','names'); if ~isempty(r) mode=['D' r.ind]; ind1=str2num(r.num1); ind2=str2num(r.num2); else mode='j1-j2'; r=regexp(str_civ,'^j= (?[a-z])-(?[a-z])','names'); if ~isempty(r) NomTypeNc='_1ab'; else r=regexp(str_civ,'^j= (?[A-Z])-(?[A-Z])','names'); if ~isempty(r) NomTypeNc='_1AB'; else r=regexp(str_civ,'^j= (?\d+)-(?\d+)','names'); if ~isempty(r) NomTypeNc='_1_1-2'; end end end if isempty(r) display('wrong pair mode input option') else ind1=stra2num(r.num1); ind2=stra2num(r.num2); end end switch mode case 'Di' i1_series=i_series-ind1;% set of first image numbers i2_series=i_series+ind2; check_bounds=i1_seriesMaxIndex_i; if isempty(j_series) NomTypeNc='_1-2'; else j1_series=j_series; j2_series=j_series; NomTypeNc='_1-2_1'; end case 'Dj' j1_series=j_series-ind1; j2_series=j_series+ind2; check_bounds=j1_seriesMaxIndex_j; NomTypeNc='_1_1-2'; otherwise %bursts i1_series=i_series(1,:);% do not sweep the j index i2_series=i_series(1,:); j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice j2_series=ind2*ones(1,size(i_series,2)); check_bounds=zeros(size(i1_series));% no limitations due to min-max indices end %INPUT: % xmid- u/2: set of apparent phys x coordinates in the ref plane, image A % ymid- v/2: set of apparent phys y coordinates in the ref plane, image A % xmid+ u/2: set of apparent phys x coordinates in the ref plane, image B % ymid+ v/2: set of apparent phys y coordinates in the ref plane, image B % XmlData: content of the xml files containing geometric calibration parameters function [z,Xphy,Yphy,Error]=shift2z(xmid, ymid, u, v,XmlData) z=0; error=0; %% first image Calib_A=XmlData{1}.GeometryCalib; R=(Calib_A.R)'; x_a=xmid- u/2; y_a=ymid- v/2; z_a=R(7)*x_a+R(8)*y_a+Calib_A.Tx_Ty_Tz(1,3); Xa=(R(1)*x_a+R(2)*y_a+Calib_A.Tx_Ty_Tz(1,1))./z_a; Ya=(R(4)*x_a+R(5)*y_a+Calib_A.Tx_Ty_Tz(1,2))./z_a; A_1_1=R(1)-R(7)*Xa; A_1_2=R(2)-R(8)*Xa; A_1_3=R(3)-R(9)*Xa; A_2_1=R(4)-R(7)*Ya; A_2_2=R(5)-R(8)*Ya; A_2_3=R(6)-R(9)*Ya; Det=A_1_1.*A_2_2-A_1_2.*A_2_1; Dxa=(A_1_2.*A_2_3-A_2_2.*A_1_3)./Det; Dya=(A_2_1.*A_1_3-A_1_1.*A_2_3)./Det; %% second image %loading shift angle Calib_B=XmlData{2}.GeometryCalib; R=(Calib_B.R)'; x_b=xmid+ u/2; y_b=ymid+ v/2; z_b=R(7)*x_b+R(8)*y_b+Calib_B.Tx_Ty_Tz(1,3); Xb=(R(1)*x_b+R(2)*y_b+Calib_B.Tx_Ty_Tz(1,1))./z_b; Yb=(R(4)*x_b+R(5)*y_b+Calib_B.Tx_Ty_Tz(1,2))./z_b; B_1_1=R(1)-R(7)*Xb; B_1_2=R(2)-R(8)*Xb; B_1_3=R(3)-R(9)*Xb; B_2_1=R(4)-R(7)*Yb; B_2_2=R(5)-R(8)*Yb; B_2_3=R(6)-R(9)*Yb; Det=B_1_1.*B_2_2-B_1_2.*B_2_1; Dxb=(B_1_2.*B_2_3-B_2_2.*B_1_3)./Det; Dyb=(B_2_1.*B_1_3-B_1_1.*B_2_3)./Det; %% result Den=(Dxb-Dxa).*(Dxb-Dxa)+(Dyb-Dya).*(Dyb-Dya); mfx=(XmlData{1}.GeometryCalib.fx_fy(1)+XmlData{2}.GeometryCalib.fx_fy(1))/2; mfy=(XmlData{1}.GeometryCalib.fx_fy(2)+XmlData{2}.GeometryCalib.fx_fy(2))/2; mtz=(XmlData{1}.GeometryCalib.Tx_Ty_Tz(1,3)+XmlData{2}.GeometryCalib.Tx_Ty_Tz(1,3))/2; %Error=(sqrt(mfx^2+mfy^2)/(2*sqrt(2)*mtz)).*(((Dyb-Dya).*(-u)-(Dxb-Dxa).*(-v))./sqrt(Den)); Error=(((Dyb-Dya).*(-u)-(Dxb-Dxa).*(-v))./sqrt(Den)); z=((Dxb-Dxa).*(-u)+(Dyb-Dya).*(-v))./Den; xnew(1,:)=Dxa.*z+x_a; xnew(2,:)=Dxb.*z+x_b; ynew(1,:)=Dya.*z+y_a; ynew(2,:)=Dyb.*z+y_b; Xphy=mean(xnew,1); Yphy=mean(ynew,1);