%'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, (several5.804 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 % 900 % .IndexRange: set the file or frame indices on which the action must be performseriesed % .FieldTransform: .TransformName: name of the select39ed 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 % uvmat .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 2008-2022, 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=sliding_average(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 mseriesax (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 object39(option 'off'/'on', ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.tfilter';%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 %% 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)series if isfield(Param,'InputFields') InputFields{1}=Param.InputFields; end5.804 nbfiles=0; nbmissing=0; %% initialisation manip Coriolis char_index=regexp(SubDir{1},'waves_L1_'); switch(SubDir{1}(char_index+9)) case '1' amplitude=2.5 %oscillation amplitude T=24.46; t0=3 ;% dt=0.5 s, torus at its max x at the beginning of motion, i0=7 case '2' amplitude=5 %oscillation amplitude T=24.47; t0=8.5; % dt=1/3 s -> image index of starting motion = 26, % torus at its max x at the beginning of motion case '3' amplitude=10 %oscillation amplitude T=24.45; t0=6.5-T/2;% dt=0.25, torus at its minimum x at the beginning of motion case '4' amplitude=15 %oscillation amplitude T=24.48; t0=3.4; %dt=0.2 -> i0=18 image index of starting motion, % torus at its max x at the beginning of motion end %NbPeriod=2; %number of periods for the sliding average NbPeriod=4; %number of periods for the sliding average omega=2*2*pi/T;%harmonic Lscale=15;%diameter of the torus, length scale for normalisation Uscale=amplitude*omega; DataOut.ListGlobalAttribute= {'Conventions','Time'}; DataOut.Conventions='uvmat'; DataOut.ListVarName={'coord_y','coord_x','Umean','Vmean','Ucos','Vcos','Usin','Vsin','DUDXsin','DUDXcos','DUDYsin','DVDXsin','DVDXcos'... ,'DVDYsin','Ustokes','Vstokes'}; DataOut.VarDimName={'coord_y','coord_x',{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},... {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},... {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}}; %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% % First get time % [Data,tild,errormsg]=nc2struct(filecell{1,1}); Time_1=Data.Time; if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) return end [Data,tild,errormsg]=nc2struct(filecell{1,end}); Time_end=Data.Time; dt=(Time_end-Time_1)/(NbField-1); %time interval NpTime=round(NbPeriod*T/dt+1); OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device)); RootFileOut=RootFile{1}; NomTypeOut='_1'; %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% disp('loop for filtering 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,~] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); %%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% if index==1 %first field DataOut.coord_x=Field.coord_x/Lscale; DataOut.coord_y=Field.coord_y/Lscale; npy=numel(DataOut.coord_y); npx=numel(DataOut.coord_x); Umean=zeros(NpTime,npy,npx); Vmean=zeros(NpTime,npy,npx); Ucos=zeros(NpTime,npy,npx); Vcos=zeros(NpTime,npy,npx); Usin=zeros(NpTime,npy,npx); Vsin=zeros(NpTime,npy,npx); DUDXcos=zeros(NpTime,npy,npx); DUDXsin=zeros(NpTime,npy,npx); DUDYsin=zeros(NpTime,npy,npx); DVDXcos=zeros(NpTime,npy,npx); DVDXsin=zeros(NpTime,npy,npx); DVDYsin=zeros(NpTime,npy,npx); end Time(index)=Field.Time-t0;%time from the start of the motion Umean=circshift(Umean,[-1 0 0]); %shift U by ishift along the first index Vmean=circshift(Vmean,[-1 0 0]); %shift U by ishift along the first index Ucos=circshift(Ucos,[-1 0 0]); %shift U by ishift along the first index Vcos=circshift(Vcos,[-1 0 0]); %shift U by ishift along the first index Usin=circshift(Usin,[-1 0 0]); %shift U by ishift along the first index Vsin=circshift(Vsin,[-1 0 0]); %shift U by ishift along the first index DUDXcos=circshift(DUDXcos,[-1 0 0]); DUDXsin=circshift(DUDXsin,[-1 0 0]); DUDYsin=circshift(DUDYsin,[-1 0 0]); DVDXcos=circshift(DVDXcos,[-1 0 0]); DVDXsin=circshift(DVDXsin,[-1 0 0]); DVDYsin=circshift(DVDYsin,[-1 0 0]); Umean(end,:,:)=Field.U; Vmean(end,:,:)=Field.V; Ucos(end,:,:)=Field.U*cos(omega*Time(index)); Vcos(end,:,:)=Field.V*cos(omega*Time(index)); Usin(end,:,:)=Field.U*sin(omega*Time(index)); Vsin(end,:,:)=Field.V*sin(omega*Time(index)); DUDXcos(end,:,:)=Field.DUDX*cos(omega*Time(index)); DUDXsin(end,:,:)=Field.DUDX*sin(omega*Time(index)); DUDYsin(end,:,:)=Field.DUDY*sin(omega*Time(index));% ParamOut=[];%default output DVDXcos(end,:,:)=Field.DVDX*cos(omega*Time(index)); DVDXsin(end,:,:)=Field.DVDX*sin(omega*Time(index)); DVDYsin(end,:,:)=Field.DVDY*sin(omega*Time(index)); DataOut.Time=(Time(index)-(NpTime-1)*dt/2)/T;%time inperiods from the beginning of the oscillation (torus at max abscissa) DataOut.Umean=(1/Uscale)*squeeze(nanmean(Umean,1)); DataOut.Vmean=(1/Uscale)*squeeze(nanmean(Vmean,1)); DataOut.Ucos=2*(1/Uscale)*squeeze(nanmean(Ucos,1)); DataOut.Vcos=2*(1/Uscale)*squeeze(nanmean(Vcos,1)); DataOut.Usin=2*(1/Uscale)*squeeze(nanmean(Usin,1)); DataOut.Vsin=2*(1/Uscale)*squeeze(nanmean(Vsin,1)); DataOut.DUDXcos=2*squeeze(nanmean(DUDXcos,1)); DataOut.DUDXsin=2*squeeze(nanmean(DUDXsin,1)); DataOut.DUDYsin=2*squeeze(nanmean(DUDYsin,1)); DataOut.DVDXcos=2*squeeze(nanmean(DVDXcos,1)); DataOut.DVDXsin=2*squeeze(nanmean(DVDXsin,1)); DataOut.DVDYsin=2*squeeze(nanmean(DVDYsin,1)); DataOut.Ustokes=(1/omega)*(1/Uscale)*(DataOut.Ucos.*DataOut.DUDXsin+DataOut.Vcos.*DataOut.DUDYsin); DataOut.Vstokes=(1/omega)*(1/Uscale)*(DataOut.Ucos.*DataOut.DVDXsin+DataOut.Vcos.*DataOut.DVDYsin); % writing the result file as netcdf file i1=i1_series{1}(index); OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeOut,i1); errormsg=struct2nc(OutputFile, DataOut); if isempty(errormsg) disp([OutputFile ' written']) else disp(errormsg) end end