%'turb_correlation_time': calculate the time correlation function at each point %------------------------------------------------------------------------ % function ParamOut=turb_correlation_time(Param) % %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% % %OUTPUT % ParamOut: sets options in the GUI series.fig needed for the function % %INPUT: % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. % In batch mode, Param is the name of the corresponding xml file containing the same information % when Param.Action.RUN=0 (as activated when the current Action is selected % in series), the function ouput paramOut set the activation of the needed GUI elements % % Param contains the elements:(use the menu bar command 'export/GUI config' in series to % see the current structure Param) % .InputTable: cell of input file names, (several lines for multiple input) % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} % .OutputSubDir: name of the subdirectory for data outputs % .OutputDirExt: directory extension for data outputs % .Action: .ActionName: name of the current activated function % .ActionPath: path of the current activated function % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct % .RUN =0 for GUI input, =1 for function activation % .RunMode='local','background', 'cluster': type of function use % % .IndexRange: set the file or frame indices on which the action must be performed % .FieldTransform: .TransformName: name of the selected transform function % .TransformPath: path of the selected transform function % .InputFields: sub structure describing the input fields withfields % .FieldName: name(s) of the field % .VelType: velocity type % .FieldName_1: name of the second field in case of two input series % .VelType_1: velocity type of the second field in case of two input series % .Coord_y: name of y coordinate variable % .Coord_x: name of x coordinate variable % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %======================================================================= % Copyright 2008-2019, 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 ParamOut=turb_correlation_time(Param) %% set the input elements needed on the GUI series when the action is selected in the menu ActionName if isstruct(Param) && isequal(Param.Action.RUN,0) ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) ParamOut.NbSlice=1; %nbre of slices ('off' by default) ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) ParamOut.FieldTransform = 'on';%can use a transform function ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.corr_t';%set the output dir extension ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice % filecell=get_file_series(Param);%check existence of the first input file % if ~exist(filecell{1,1},'file') % msgbox_uvmat('WARNING','the first input file does not exist') % end return end %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% ParamOut=[];%default output %% 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 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 %% define the directory for result file (with path=RootPath{1}) OutputDir=[Param.OutputSubDir Param.OutputDirExt]; %% root input file(s) name, type and index series RootPath=Param.InputTable(:,1); RootFile=Param.InputTable(:,3); SubDir=Param.InputTable(:,2); NomType=Param.InputTable(:,4); FileExt=Param.InputTable(:,5); [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); %%%%%%%%%%%% % The cell array filecell is the list of input file names, while % filecell{iview,fileindex}: % iview: line in the table corresponding to a given file series % fileindex: file index within the file series, % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices %%%%%%%%%%%% NbView=1 : a single input series NbView=numel(i1_series);%number of input file series (lines in InputTable) NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) NbField_i=size(i1_series{1},2); %nb of fields for the i index NbField=NbField_j*NbField_i; %total number of fields NpTime=256;% max number of times for each side of the time correlation fct NpTime=min(NpTime,floor(NbField/4)); %nbre of points for the correlation fct on each side of 0 %% determine the file type on each line from the first input file ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView if ~exist(filecell{iview,1}','file') msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) return end [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); FileType{iview}=FileInfo{iview}.FileType; CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files if ~isempty(j1_series{iview}) frame_index{iview}=j1_series{iview}; else frame_index{iview}=i1_series{iview}; end end %% calibration data and timing: read the ImaDoc files XmlData=[]; [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); if size(time,1)>1 diff_time=max(max(diff(time))); if diff_time>0 msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) end end %% coordinate transform or other user defined transform transform_fct='';%default if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) addpath(Param.FieldTransform.TransformPath) transform_fct=str2func(Param.FieldTransform.TransformName); rmpath(Param.FieldTransform.TransformPath) end %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% % EDIT FROM HERE %% check the validity of input file types if CheckImage{1} FileExtOut='.png'; % write result as .png images for image inputs elseif CheckNc{1} FileExtOut='.nc';% write result as .nc files for netcdf inputs else msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) return end %% settings for the output file NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file first_i=i1_series{1}(1); last_i=i1_series{1}(end); if isempty(j1_series{1})% if there is no second index j first_j=1;last_j=1; else first_j=j1_series{1}(1); last_j=j1_series{1}(end); end %% Set field names and velocity types InputFields{1}=[];%default (case of images) if isfield(Param,'InputFields') InputFields{1}=Param.InputFields; end nbfiles=0; nbmissing=0; %initialisation DataOut.ListGlobalAttribute= {'Conventions'}; DataOut.Conventions='uvmat'; DataOut.ListVarName={'delta_t','coord_y','coord_x','UUCorr' , 'VVCorr','UVCorr','Counter'}; DataOut.VarDimName={'delta_t','coord_y','coord_x',... {'delta_t','coord_y','coord_x'},{'delta_t','coord_y','coord_x'},{'delta_t','coord_y','coord_x'},{'delta_t','coord_y','coord_x'}}; %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% % First get mean values % disp('loop for mean started') Time=zeros(1,NbField); for index=1:NbField update_waitbar(WaitbarHandle,index/NbField) if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') break end [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); if index==1 %first field if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) return elseif ~isfield(Field,'U')||~isfield(Field,'V') disp_uvmat('ERROR','this function requires the velocity components U and V as input',checkrun) return elseif ~isfield(Field,'Time') disp_uvmat('ERROR','the attribute Time needs to be defined as input',checkrun) return end [npy,npx]=size(Field.U); UMean=zeros(npy,npx); VMean=zeros(npy,npx); Counter=false(npy,npx); % transcripts the global attributes if isfield(Field,'ListGlobalAttribute') DataOut.ListGlobalAttribute= Field.ListGlobalAttribute; for ilist=1:numel(Field.ListGlobalAttribute) AttrName=Field.ListGlobalAttribute{ilist}; DataOut.(AttrName)=Field.(AttrName); end end end Time(index)=Field.Time; FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U Field.U(FF)=0;% set to 0 the nan values, Field.V(FF)=0; UMean=UMean+Field.U; VMean=VMean+Field.V; Counter=Counter+~FF; end UMean=UMean./Counter; VMean=VMean./Counter; %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% disp('loop for correlation started') for index=1:NbField update_waitbar(WaitbarHandle,index/NbField) if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') break end [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% if index==1 %first field [npy,npx]=size(Field.U); dt=diff(Time); Maxdt=max(dt); Mindt=min(dt); if Maxdt-Mindt>0.001*Maxdt disp_uvmat('ERROR','the time increment between fields is not constant',checkrun) return else dt=(Maxdt+Mindt)/2; end DataOut.delta_t=(0:dt:dt*NpTime)'; DataOut.coord_x=Field.coord_x; DataOut.coord_y=Field.coord_y; DataOut.UUCorr=zeros(NpTime+1,npy,npx); DataOut.VVCorr=zeros(NpTime+1,npy,npx); DataOut.UVCorr=zeros(NpTime+1,npy,npx); DataOut.Counter=zeros(NpTime+1,npy,npx); U_shift=zeros(NpTime+1,npy,npx); V_shift=zeros(NpTime+1,npy,npx); FF_shift=zeros(NpTime+1,npy,npx); UUCorr=zeros(NpTime+1,npy,npx); VVCorr=zeros(NpTime+1,npy,npx); UVCorr=zeros(NpTime+1,npy,npx); FFCorr=false(NpTime+1,npy,npx); end Field.U=Field.U-UMean; Field.V=Field.V-VMean; FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U Field.U(FF)=0;% set to 0 the nan values,'delta_x' Field.V(FF)=0; if index<=NpTime+1 U_shift(NpTime+2-index,:,:)=Field.U; V_shift(NpTime+2-index,:,:)=Field.V; FF_shift(NpTime+2-index,:,:)=FF; else U_shift=circshift(U_shift,[1 0 0]); %shift U by ishift along the first index V_shift=circshift(V_shift,[1 0 0]); %shift U by ishift along the first index FF_shift=circshift(FF_shift,[1 0 0]); %shift U by ishift along the first index U_shift(1,:,:)=Field.U; V_shift(1,:,:)=Field.V; FF_shift(1,:,:)=FF; end for ishift=1:NpTime+1% calculate the field U shifted UUCorr(ishift,:,:)=Field.U.*squeeze(U_shift(ishift,:,:)); VVCorr(ishift,:,:)=Field.V.*squeeze(V_shift(ishift,:,:)); UVCorr(ishift,:,:)=Field.U.*squeeze(V_shift(ishift,:,:)); FFCorr(ishift,:,:)=FF | squeeze(FF_shift(ishift,:,:)); end DataOut.UUCorr=DataOut.UUCorr+UUCorr; DataOut.VVCorr=DataOut.VVCorr+VVCorr; DataOut.UVCorr=DataOut.UVCorr+UVCorr; DataOut.Counter=DataOut.Counter+~FFCorr; end %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero (to avoid NaN) DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter; DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter; DataOut.UVCorr=DataOut.UVCorr./DataOut.Counter; % DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean % DataOut.VMean=DataOut.VMean./DataOut.Counter; % normalize the mean % U2Mean=U2Mean./DataOut.Counter; % normalize the mean % V2Mean=V2Mean./DataOut.Counter; % normalize the mean % UVMean=UVMean./DataOut.Counter; % normalize the mean % U2Mean_1=U2Mean_1./Counter_1; % normalize the mean % V2Mean_1=V2Mean_1./Counter_1; % normalize the mean % DataOut.u2Mean=U2Mean-DataOut.UMean.*DataOut.UMean; % normalize the meanFFCorr % DataOut.v2Mean=V2Mean-DataOut.VMean.*DataOut.VMean; % normalize the mean % DataOut.uvMean=UVMean-DataOut.UMean.*DataOut.VMean; % normalize the mean \ % DataOut.u2Mean_1=U2Mean_1-DataOut.UMean.*DataOut.UMean; % normalize the mean % DataOut.v2Mean_1=V2Mean_1-DataOut.VMean.*DataOut.VMean; % normalize the mean %% calculate the profiles % npx=numel(DataOut.coord_x); % band=ceil(npx/5) :floor(4*npx/5);% keep only the central band % for ivar=3:numel(DataOut.ListVarName)-1 % VarName=DataOut.ListVarName{ivar};% name of the variable % DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Profile']}];%append the name of the profile variable % DataOut.VarDimName=[DataOut.VarDimName {'coord_y'}]; % DataOut.([VarName 'Profile'])=mean(DataOut.(VarName)(:,band),2); %take the mean profile of U, excluding the edges % end %% writing the result file as netcdf file OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); %case of netcdf input file , determine global attributes errormsg=struct2nc(OutputFile,DataOut); %save result file if isempty(errormsg) disp([OutputFile ' written']); else disp(['error in writting result file: ' errormsg]) end %% open the result file with uvmat (in RUN mode) if checkrun uvmat(OutputFile)% open the last result file with uvmat end