%'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) % %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: Matlab structure of input parameters % Param contains info of the GUI series using the fct read_GUI. % Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation % Param.InputTable: sets the input file(s) % if absent, the fct looks for input data in Param.ActionInput (test mode) % Param.OutputSubDir: sets the folder name of output file(s, % if absent no file is produced, result in the output structure Data (test mode) % Param.ActionInput: substructure with the parameters provided by the GUI civ_input % .Civ1: parameters for civ1 % .Fix1: parameters for fix1 % .Patch1: % .Civ2: for civ2 % .Fix2: % .Patch2: %======================================================================= % Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr % % This file 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 (see LICENSE.txt) for more details. %======================================================================= function [Data,errormsg,result_conv]= civ_series(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='off';% 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) if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices')&& strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input) end 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='on';% 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 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='.civ';%set the output dir extension Data.OutputSubDirMode='last'; %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 %% test input if ~isfield(Param,'ActionInput') disp_uvmat('ERROR','no parameter set for PIV',checkrun) return end iview_A=0;%default values NbField=1; RUNHandle=[]; CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved) CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced) %% input files and indexing (skipped in Test mode) if CheckInputFile 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 MaxIndex_i=Param.IndexRange.MaxIndex_i; MinIndex_i=Param.IndexRange.MinIndex_i; MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') MaxIndex_j=Param.IndexRange.MaxIndex_j; MinIndex_j=Param.IndexRange.MinIndex_j; end if isfield(Param,'InputTable') [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); iview_A=0;% series index (iview) for the first image series iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) if Param.ActionInput.CheckCiv1 iview_A=1;% usual PIV, the image series is on the first line of the table elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line iview_A=2;% the second line is used for the input images of Civ2 end if strcmp(Param.ActionInput.ListCompareMode,'shift') iview_B=iview_A+1; % the second image series is on the next line of the input table end if iview_A~=0 RootPath_A=Param.InputTable{iview_A,1}; RootFile_A=Param.InputTable{iview_A,3}; SubDir_A=Param.InputTable{iview_A,2}; NomType_A=Param.InputTable{iview_A,4}; FileExt_A=Param.InputTable{iview_A,5}; if iview_B==0 iview_B=iview_A;% the second image series is the same as the first end RootPath_B=Param.InputTable{iview_B,1}; RootFile_B=Param.InputTable{iview_B,3}; SubDir_B=Param.InputTable{iview_B,2}; NomType_B=Param.InputTable{iview_B,4}; FileExt_B=Param.InputTable{iview_B,5}; end PairCiv2=''; switch Param.ActionInput.ListCompareMode case 'PIV' PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair end if iview_A==1% if Civ1 is performed [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); if ~isempty(PairCiv2) [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1)); check_bounds=check_bounds | check_bounds_Civ2; end else% we start from an existing Civ1 file i1_series_Civ1=i1_series{1}; i2_series_Civ1=i2_series{1}; j1_series_Civ1=j1_series{1}; j2_series_Civ1=j2_series{1}; NomTypeNc=Param.InputTable{1,4}; if ~isempty(PairCiv2) [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2)); end end case 'displacement' i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); i2_series_Civ1=i1_series{1};i2_series_Civ2=i1_series{1}; j1_series_Civ1=ones(size(i1_series{1}));% first j index is 1 if isempty(j1_series_Civ1) j2_series_Civ1=ones(size(i1_series{1})); else j2_series_Civ1=j1_series_Civ1; end i1_series_Civ2=i1_series_Civ1; j1_series_Civ2=j1_series_Civ1; j2_series_Civ2=j2_series_Civ1; NomTypeNc=Param.InputTable{1,4}; case 'PIV volume' % TODO, TODO end 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 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=''; if CheckOutputFile OutputDir=[Param.OutputSubDir Param.OutputDirExt]; end end %% prepare output 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 check_civx=0;%default %% get timing from the ImaDoc file or input video if iview_A~=0 XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A); Time=[]; if ~isempty(XmlFileName) XmlData=imadoc2struct(XmlFileName); if isfield(XmlData,'Time') Time=XmlData.Time; TimeSource='xml'; end if isfield(XmlData,'Camera') if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) NbSlice_calib{iview}=XmlData.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.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) TimeUnit=XmlData.Camera.TimeUnit; end end end 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 +0.001 index j by default %MinIndex_i=min(i1_series_Civ1); MaxIndex_i=max(i2_series_Civ1); %MinIndex_j=min(j1_series_Civ1); MaxIndex_j=max(j2_series_Civ1); Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); Time=Time+0.001*ones(MaxIndex_i,1)*(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 end %%%%% MAIN LOOP %%%%%% maskname='';% initiate the mask name tic; CheckOverwrite=1;%default if isfield(Param,'CheckOverwrite') CheckOverwrite=Param.CheckOverwrite; end for ifield=1:NbField if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series (checkrun=1) update_waitbar(WaitbarHandle,ifield/NbField) if checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') break end end if CheckInputFile if iview_A==0 % no nc file has been entered ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); else% an existing nc file has been entered if iview_A==1% if Civ1 is performed Civ1Dir=OutputDir; else Civ1Dir=Param.InputTable{1,2}; end if strcmp(Param.ActionInput.ListCompareMode,'PIV') ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... j1_series_Civ1(ifield),j2_series_Civ1(ifield)); else ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... j1_series_Civ1(ifield),j2_series_Civ1(ifield)); end end ncfile_out=ncfile;% by default if isfield (Param.ActionInput,'Civ2') i1_civ2=i1_series_Civ2(ifield); i2_civ2=i1_civ2; if ~isempty(i2_series_Civ2) i2_civ2=i2_series_Civ2(ifield); end j1_civ2=1; if ~isempty(j1_series_Civ2) j1_civ2=j1_series_Civ2(ifield); end j2_civ2=i1_civ2; if ~isempty(j2_series_Civ2) j2_civ2=j2_series_Civ2(ifield); end if strcmp(Param.ActionInput.ListCompareMode,'PIV') ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2); else % displacement ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2); end end if ~CheckOverwrite && exist(ncfile_out,'file') disp(['existing output file ' ncfile_out ' already exists, skip to next field']) continue% skip iteration if the mode overwrite is desactivated and the result file already exists end end %% Civ1 % if Civ1 computation is requested if isfield (Param.ActionInput,'Civ1') if CheckInputFile disp('civ1 started') end par_civ1=Param.ActionInput.Civ1; if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) try ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); if strcmp(FileInfo_A.FileType,'netcdf')% case of input images in format netcdf FieldName_A=Param.InputFields.FieldName; [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); par_civ1.ImageA=DataIn.(FieldName_A); else % usual image formats for image A [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); end ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); if strcmp(FileInfo_B.FileType,'netcdf') % case of input images in format netcdf FieldName_B=Param.InputFields.FieldName; [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); par_civ1.ImageB=DataIn.(FieldName_B); else % usual image formats for image B [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); end catch ME % display errors in reading input images if ~isempty(ME.message) disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) return end end 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))'; list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list 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 if strcmp(Param.ActionInput.ListCompareMode,'displacement') Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading else Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1); end 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; end % set the list of variables Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; Data.VarAttribute{1}.Role='coord_x'; Data.VarAttribute{2}.Role='coord_y'; Data.VarAttribute{3}.Role='vector_x'; Data.VarAttribute{4}.Role='vector_y'; Data.VarAttribute{5}.Role='warnflag'; if par_civ1.CheckMask&&~isempty(par_civ1.Mask) if strcmp(maskname,par_civ1.Mask)% mask exist, not already read in civ1 par_civ1.Mask=mask; %use mask already opened else try par_civ1.Mask=imread(par_civ1.Mask);%update the mask, an store it for future use catch ME if ~isempty(ME.message) errormsg=['error reading input image: ' ME.message]; disp_uvmat('ERROR',errormsg,checkrun) return end end mask=par_civ1.Mask; maskname=par_civ1.Mask; end end if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume') Data.ListVarName=[Data.ListVarName 'Civ1_Z']; Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[]; for ivol=1:NbSlice % caluclate velocity data (y and v in indices, reverse to y component) [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) return end Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)]; end else %usual PIV % caluclate velocity data (y and v in indices, reverse to y component) [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) return end Data.Civ1_X=reshape(xtable,[],1); Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1); Data.Civ1_U=reshape(utable,[],1); Data.Civ1_V=reshape(-vtable,[],1); Data.Civ1_C=reshape(ctable,[],1); Data.Civ1_F=reshape(F,[],1); end else% we use existing Civ1 data if exist('ncfile','var') CivFile=ncfile; [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) return end [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file elseif isfield(Param,'Civ1_X') Data.ListGlobalAttribute={}; Data.ListVarName={}; Data.VarDimName={}; Data.Civ1_X=Param.Civ1_X; Data.Civ1_Y=Param.Civ1_Y; Data.Civ1_U=Param.Civ1_U; Data.Civ1_V=Param.Civ1_V; Data.Civ1_FF=Param.Civ1_FF; end end %% Fix1 if isfield (Param.ActionInput,'Fix1') disp('fix1 started') 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 list_param=fieldnames(Param.ActionInput.Fix1)'; Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before each string in ListFixParam %indicate the values of all the global attributes in the output data for ilist=1:length(list_param) Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist}); end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param]; 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=int8(fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V)); Data.CivStage=2; end %% Patch1 if isfield (Param.ActionInput,'Patch1') disp('patch1 started') if check_civx errormsg='Civ Matlab input needed for patch'; disp_uvmat('ERROR',errormsg,checkrun) return end % record the processing parameters of Patch1 as global attributes in the result nc file list_param=fieldnames(Param.ActionInput.Patch1)'; list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before each parameter name for ilist=1:length(list_param) Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist}); end Data.CivStage=3;% record the new state of processing Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param]; % list the variables to record 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=Data.Civ1_U; % zeros(size(Data.Civ1_X)); Data.Civ1_V_smooth=Data.Civ1_V; %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 % perform Patch calculation using the UVMAT fct 'filter_tps' [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;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other Data.Civ1_V_smooth(ind_good)=Vres; Data.Civ1_FF(ind_good)=int8(FFres); disp('patch1 performed') end %% Civ2 if isfield (Param.ActionInput,'Civ2') disp('civ2 started') par_civ2=Param.ActionInput.Civ2; if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) par_civ2.ImageA=[]; par_civ2.ImageB=[]; % i1_civ2=i1_series_Civ2(ifield); % i2_civ2=i1_civ2; % if ~isempty(i2_series_Civ2) % i2_civ2=i2_series_Civ2(ifield); % end % j1_civ2=1; % if ~isempty(j1_series_Civ2) % j1_civ2=j1_series_Civ2(ifield); % end % j2_civ2=i1_civ2; % if ~isempty(j2_series_Civ2) % j2_civ2=j2_series_Civ2(ifield); % end ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); 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_civ2,[],j2_civ2); 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 % if strcmp(Param.ActionInput.ListCompareMode,'PIV') % ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2); % else % displacement % ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2,[],j2); % end 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 end % get the guess from patch1 or patch2 (case 'CheckCiv3') if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from patch2 SubRange= Data.Civ2_SubRange; NbCentres=Data.Civ2_NbCentres; Coord_tps=Data.Civ2_Coord_tps; U_tps=Data.Civ2_U_tps; V_tps=Data.Civ2_V_tps; CivStage=Data.CivStage;%store the current CivStage Civ1_Dt=Data.Civ2_Dt; Data=[];%reinitialise the result structure Data 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=CivStage+1;%update the current civStage after reinitialisation of Data Data.ListVarName={}; Data.VarDimName={}; else % get the guess from patch1 SubRange= Data.Civ1_SubRange; NbCentres=Data.Civ1_NbCentres; Coord_tps=Data.Civ1_Coord_tps; U_tps=Data.Civ1_U_tps; V_tps=Data.Civ1_V_tps; Civ1_Dt=Data.Civ1_Dt; Data.CivStage=4; end else SubRange= par_civ2.Civ1_SubRange; NbCentres=par_civ2.Civ1_NbCentres; Coord_tps=par_civ2.Civ1_Coord_tps; U_tps=par_civ2.Civ1_U_tps; V_tps=par_civ2.Civ1_V_tps; Civ1_Dt=par_civ2.Civ1_Dt; Civ2_Dt=par_civ2.Civ1_Dt; Data.ListVarName={}; Data.VarDimName={}; 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);% nbre of interpolated values at each grid point (from the different patch subdomains) 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(SubRange,3); for isub=1:NbSubDomain% for each sub-domain of Patch1 nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &... par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain if ~isempty(ind_sel) epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids) ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap) EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1 Shifty(ind_sel)=Shifty(ind_sel)+EM*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*U_tps(1:nbvec_sub+3,isub); DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub); DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub); DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub); end end end if par_civ2.CheckMask&&~isempty(par_civ2.Mask) if strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 par_civ2.Mask=mask; %use mask already opened else par_civ2.Mask=imread(par_civ2.Mask);%update the mask, and store it for future use mask=par_civ2.Mask; maskname=par_civ2.Mask; end end if CheckInputFile % else Dt given by par_civ2 if strcmp(Param.ActionInput.ListCompareMode,'displacement') Civ1_Dt=1; Civ2_Dt=1; else Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1); end end par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; % shift the grid points by half the expected shift to provide the correlation box position in image A 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]; 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 image indices, reverse to y component) [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2); list_param=(fieldnames(Param.ActionInput.Civ2))'; list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list 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 if exist('ImageName_A','var') Data.Civ2_ImageA=ImageName_A; Data.Civ2_ImageB=ImageName_B; if strcmp(Param.ActionInput.ListCompareMode,'displacement') Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading else Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2; Data.Civ2_Dt=Civ2_Dt; end end 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); % define the Civ2 variable (if Civ2 data are not replaced from previous calculation) if isempty(find(strcmp('Civ2_X',Data.ListVarName),1)) 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'; end 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); disp('civ2 performed') elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data if exist('ncfile','var') CivFile=ncfile; [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) return end elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode) Data.ListGlobalAttribute={}; Data.ListVarName={}; Data.VarDimName={}; Data.Civ2_X=Param.Civ2_X; Data.Civ2_Y=Param.Civ2_Y; Data.Civ2_U=Param.Civ2_U; Data.Civ2_V=Param.Civ2_V; Data.Civ2_FF=Param.Civ2_FF; end end %% Fix2 if isfield (Param.ActionInput,'Fix2') disp('fix2 started') list_param=fieldnames(Param.ActionInput.Fix2)'; Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before each string in ListFixParam %indicate the values of all the global attributes in the output data for ilist=1:length(list_param) Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist}); end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param]; % % 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') disp('patch2 started') list_param=fieldnames(Param.ActionInput.Patch2)'; list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before each string in ListFixParam %indicate the values of all the global attributes in the output data for ilist=1:length(list_param) Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist}); end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param]; 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=Data.Civ2_U; Data.Civ2_V_smooth=Data.Civ2_V; 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; disp('patch2 performed') end %% write result in a netcdf file if requested if CheckOutputFile errormsg=struct2nc(ncfile_out,Data); if isempty(errormsg) disp([ncfile_out ' written']) %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc else disp(errormsg) end disp(['ellapsed time ' num2str(toc/60,2) ' minutes']) 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: % .ImageA: first image for correlation (matrix) % .ImageB: second image for correlation(matrix) % .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y % .SearchBoxSize: 1,2 vector giving the size of the search box in x and y % .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y % .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max % .ImageWidth: nb of pixels of the image in x % .Dx, Dy: mesh for the PIV calculation % .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A % .Mask: name of a mask file or mask image matrix itself % .MinIma: thresholds for image luminosity % .MaxIma % .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform) % .DUDX: matrix of deformation obtained from patch at each grid point % .DUDY % .DVDX: % .DVDY function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ) %% prepare measurement grid if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates) par_civ.Grid=dlmread(par_civ.Grid); par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) end % else par_civ.Grid is already an array, no action here else% automatic grid in x, y image coordinates 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;% first automatic grid point at half the mesh Dy 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);% increases with array index 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));%use the input shift estimate, rounded to the next integer value 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 %% Array initialisation and default output if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation) xtable=round(par_civ.Grid(:,1)+0.5)-0.5; ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes utable=shiftx;%zeros(nbvec,1); vtable=shifty;%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);% read the mask if not allready done 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_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); % par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined area % par_civ.ImageB(check_undefined)=0;% 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 (x 4 in each direction) par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max) end if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given) 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);% j index for the middle of the correlation box in the image A 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 if checkmask 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 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 image B 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; % utable(ivec)=0; vtable(ivec)=0; 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 F(ivec)~=3 if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) F(ivec)=3; %threshold on image maximum elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) F(ivec)=3; end if F(ivec)==3 utable(ivec)=0; vtable(ivec)=0; else %mask if checkmask image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts image2_crop=(image2_crop-image2_mean).*~mask2_crop; else image1_crop=(image1_crop-image1_mean); image2_crop=(image2_crop-image2_mean); end %deformation 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)); %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);% srt 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); else [vector,F(ivec)] = quadr_fit(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)+0.5);% nearest image index for the middle of the vector jref=round(ytable(ivec)+0.5); % eliminate vectors located in the mask if checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( 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; disp(ME.message) end else F(ivec)=3; end end 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 % OUPUT: % vector = optimum displacement vector with subpixel correction % F =flag: =0 OK % =-2 , warning: max too close to the edge of the search box (1 pixel margin) % INPUT: % x,y: position of the maximum correlation at integer values 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 (=0 by discretisation, 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 && 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) && (y < npy) && (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]; %------------------------------------------------------------------------ % --- Find the maximum of the correlation function after quadratic interpolation function [vector,F] = quadr_fit(result_conv,x,y) [npy,npx]=size(result_conv); if x<4 || y<4 || npx-x<4 ||npy-y <4 F=-2; vector=[x y]; else F=0; x_ind=x-4:x+4; y_ind=y-4:y+4; x_vec=0.25*(x_ind-x); y_vec=0.25*(y_ind-y); [X,Y]=meshgrid(x_vec,y_vec); coord=[reshape(X,[],1) reshape(Y,[],1)]; result_conv=reshape(result_conv(y_ind,x_ind),[],1); % n=numel(X); % x=[X Y]; % X=X-0.5; % Y=Y+0.5; % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1); p = polyfitn(coord,result_conv,2); A(1,1)=2*p.Coefficients(1); A(1,2)=p.Coefficients(2); A(2,1)=p.Coefficients(2); A(2,2)=2*p.Coefficients(4); vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]'; vector=vector'-[floor(npx/2) floor(npy/2)]-1 ; % zg = polyvaln(p,coord); % figure % surf(x_vec,y_vec,reshape(zg,9,9)) % hold on % plot3(X,Y,reshape(result_conv,9,9),'o') % hold off end %'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