Index: /trunk/src/series/stereo_civ.m =================================================================== --- /trunk/src/series/stereo_civ.m (revision 834) +++ /trunk/src/series/stereo_civ.m (revision 834) @@ -0,0 +1,1033 @@ +%'civ_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 2011-2014, LEGI / CNRS UJF G-INP, 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]= stereo_civ(Param) +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 + path_series=fileparts(which('series')); + addpath(fullfile(path_series,'series')) + Data=civ_input(Param);% introduce the civ parameters using the GUI civ_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) + 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); +for iview=1:size(Param.InputTable,1) + XmlFileName=find_imadoc(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5}); + 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}) + 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}; +end +j1_series_Civ2=j1_series_Civ1; +j2_series_Civ2=j2_series_Civ1; +NomTypeNc=NomType_A; +if isempty(j1_series_Civ1) + FrameIndex_A_Civ1=i1_series_Civ1; + FrameIndex_B_Civ1=i2_series_Civ1; + j1_series_Civ1=ones(size(i1_series_Civ1)); + j2_series_Civ1=ones(size(i1_series_Civ1)); +else + FrameIndex_A_Civ1=j1_series_Civ1; + FrameIndex_B_Civ1=j2_series_Civ1; +end +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 fo 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 + + +%% Output directory +OutputDir=[Param.OutputSubDir Param.OutputDirExt]; + +Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; +Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes +Data.Program='civ_series'; +Data.CivStage=0;%default +maskname='';%default +check_civx=0;%default + +%% get timing from input video +if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% 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 + + +%%%%% MAIN LOOP %%%%%% +for ifield=1:NbField + update_waitbar(WaitbarHandle,ifield/NbField) + if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') + disp('program stopped by user') + break + end + Civ1Dir=OutputDir; + + ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... + j1_series_Civ1(ifield),j2_series_Civ1(ifield)); + %% 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); + 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=[Data.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); + if ~isempty(errormsg) + disp_uvmat('ERROR',errormsg,checkrun) + return + end + 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_civ2.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 + ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1,[],j1); + + if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) + par_civ2.ImageA=par_civ1.ImageA; + else + [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); + end + ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2,[],j2); + if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) + par_civ2.ImageB=par_civ1.ImageB; + else + [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); + end + + ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,... + j1,j2); + par_civ2.ImageWidth=FileInfo_A.Width; + par_civ2.ImageHeight=FileInfo_A.Height; + + 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 + ibx2=ceil(par_civ2.CorrBoxSize(1)/2); + iby2=ceil(par_civ2.CorrBoxSize(2)/2); + par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess + par_civ2.SearchBoxSize(2)=2*iby2+9; + Civ2_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); + par_civ2.SearchBoxShift=(Civ2_Dt/Data.Civ1_Dt)*[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; + 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.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=Civ2_Dt; + % Data.Civ2_Time=1; + % Data.Civ2_Dt=1; + 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 + + %% 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 +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); +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 ￜ 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 ￜ 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: 511ￜ515 + 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 + + + +