%'aver_stat': calculate field average over a time series %------------------------------------------------------------------------ % function ParamOut=aver_stat(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=aver_synchro(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='on'; %nbre of slices ('off' by default) ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) ParamOut.FieldName='two';% 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='on';%can use projection object(option 'off'/'on', ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.synchro';%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 def={'26'}; if isfield (Param,'ActionInput')&& isfield(Param.ActionInput,'WavePeriod') def=Param.ActionInput.WavePeriod; def={num2str(def)}; end prompt={'wave period'}; dlgTitle='primary period'; lineNo=1; answer=inputdlg(prompt,dlgTitle,lineNo,def); ParamOut.ActionInput.WavePeriod=str2num(answer{1}); 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); FileInfo=get_file_info(filecell{1,1}); FileType=FileInfo.FileType; %%%%%%%%%%%% % 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=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 input file type % if ~strcmp(FileType{1},'netcdf') % displ_uvmat('ERROR','netcdf file series with field projected on a regular mesh must be put as input') % return % end %% calibration data and timing: read the ImaDoc files [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 %% 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 % for i_slice=1:NbSlice % index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice nbfiles=0; nbmissing=0; MeanU=0; MeanV=0; MinU=0; MaxU=0; MinV=0; MaxV=0; vec_X=0; vec_Y=0; vec_U=0; %initiate the sum vec_V=0; cos1_U=0; cos1_V=0; sin1_U=0; sin1_V=0; cos2_U=0; cos2_V=0; sin2_U=0; sin2_V=0; cos3_U=0; cos3_V=0; sin3_U=0; sin3_V=0; cossub_U=0; cossub_V=0; sinsub_U=0; sigma1=2*pi/Param.ActionInput.WavePeriod;%primary wave frequency sigma2=4*pi/Param.ActionInput.WavePeriod;%harmonic 2 sigma3=6*pi/Param.ActionInput.WavePeriod;%harmonic 3 sigma_sub=pi/Param.ActionInput.WavePeriod;%subharmonic sinsub_V=0; NbField=0; vec_C=0; %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% for index=1:nbfield index update_waitbar(WaitbarHandle,index/nbfield) if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') break end % reading input file(s) [Data,tild,errormsg] = read_field(filecell{1,index},FileType,InputFields{1}); if ~isempty(errormsg) displ_uvmat('ERROR',['error of input reading: ' errormsg],checkrun); break end if ~isempty(NbSlice_calib) Data.ZIndex=mod(i1_series{1}(index)-1,NbSlice_calib{1})+1;%Zindex for phys transform end %update average FF=isnan(Data.U)|isnan(Data.V);% chceck NaN values Data.U(FF)=0;% set to zero the NaN values Data.V(FF)=0; NbField=NbField+~FF;%count the NaN values MeanU=MeanU+Data.U; MeanV=MeanV+Data.V; MaxU=(MaxU>=Data.U).*MaxU+(MaxUData.U).*Data.U; MaxV=(MaxV>=Data.V).*MaxV+(MaxVData.V).*Data.V; cos1_U=cos1_U+Data.U*cos(Data.Time*sigma1); cos1_V=cos1_V+Data.V*cos(Data.Time*sigma1); sin1_U=sin1_U+Data.U*sin(Data.Time*sigma1); sin1_V=sin1_V+Data.V*sin(Data.Time*sigma1); cos2_U=cos2_U+Data.U*cos(Data.Time*sigma2); cos2_V=cos2_V+Data.V*cos(Data.Time*sigma2); sin2_U=sin2_U+Data.U*sin(Data.Time*sigma2); sin2_V=sin2_V+Data.V*sin(Data.Time*sigma2); cos3_U=cos3_U+Data.U*cos(Data.Time*sigma3); cos3_V=cos3_V+Data.V*cos(Data.Time*sigma3); sin3_U=sin3_U+Data.U*sin(Data.Time*sigma3); sin3_V=sin3_V+Data.V*sin(Data.Time*sigma3); cossub_U=cossub_U+Data.U*cos(Data.Time*sigma_sub); cossub_V=cossub_V+Data.V*cos(Data.Time*sigma_sub); sinsub_U=sinsub_U+Data.U*sin(Data.Time*sigma_sub); sinsub_V=sinsub_V+Data.V*sin(Data.Time*sigma_sub); end %%%%%%%%%%%%%%%%%%%%%%%% Data.ListVarName={'coord_x','coord_y','MeanU','MeanV','cos1_U','cos1_V','a1_U','a1_V','a2_U','a2_V','a3_U','a3_V','asub_U','asub_V',... 'phase1_U','phase1_V','phase2_U','phase2_V','phase3_U','phase3_V','phasesub_U','phasesub_V'}; %Data.ListVarName=[{'coord_y','coord_x'} Data.ListVarName]; %Data.VarDimName={'coord_y', 'coord_x'}; for ilist=1:numel(Data.ListVarName)-2 Data.VarDimName{ilist+2}={'coord_y','coord_x'}; % Data.VarDimName{ilist}='nb_vectors'; end Data.MeanU=MeanU./NbField; Data.MeanV=MeanV./NbField; cos1_U=cos1_U./NbField; cos1_V=cos1_V./NbField; sin1_U=sin1_U./NbField; sin1_V=sin1_V./NbField; cos2_U=cos2_U./NbField; cos2_V=cos2_V./NbField; sin2_U=sin2_U./NbField; sin2_V=sin2_V./NbField; cos3_U=cos3_U./NbField; cos3_V=cos3_V./NbField; sin3_U=sin3_U./NbField; sin3_V=sin3_V./NbField; cossub_U=cossub_U./NbField; cossub_V=cossub_V./NbField; sinsub_U=sinsub_U./NbField; sinsub_V=sinsub_V./NbField; Data.cos1_U=cos1_U; Data.cos1_V=cos1_V; Data.a1_U=sqrt(2)*sqrt(cos1_U.*cos1_U+sin1_U.*sin1_U); Data.a1_V=-sqrt(2)*sqrt(cos1_V.*cos1_V+sin1_V.*sin1_V); Data.a2_U=sqrt(2)*sqrt(cos2_U.*cos2_U+sin2_U.*sin2_U); Data.a2_V=-sqrt(2)*sqrt(cos2_V.*cos2_V+sin2_V.*sin2_V); Data.a3_U=sqrt(2)*sqrt(cos3_U.*cos3_U+sin3_U.*sin3_U); Data.a3_V=-sqrt(2)*sqrt(cos3_V.*cos3_V+sin3_V.*sin3_V); Data.asub_U=sqrt(2)*sqrt(cossub_U.*cossub_U+sinsub_U.*sinsub_U); Data.asub_V=-sqrt(2)*sqrt(cossub_V.*cossub_V+sinsub_V.*sinsub_V); % clear i Data.phase1_U=(angle(cos1_U+i*sin1_U)); Data.phase1_V=angle(cos1_V+i*sin1_V); Data.phase2_U=(angle(cos2_U+i*sin2_U)); Data.phase2_V=(angle(cos2_V+i*sin2_V)); Data.phase3_U=(angle(cos3_U+i*sin3_U)); Data.phase3_V=(angle(cos3_V+i*sin3_V)); Data.phasesub_U=(angle(cossub_U+i*sinsub_U)); Data.phasesub_V=(angle(cossub_V+i*sinsub_V)); %% write the results OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','',1); errormsg=struct2nc(OutputFile,Data);% write the output file if isempty(errormsg) disp_uvmat('CONFIRMATION',[OutputFile ' successfully written'],checkrun) else disp_uvmat('ERROR',errormsg,checkrun) end %% open the result file with uvmat (in RUN mode) % if checkrun % uvmat(OutputFile)% open the last result file with uvmat % end '#### THE END ####'