Index: trunk/src/series/civ_series.m =================================================================== --- trunk/src/series/civ_series.m (revision 1089) +++ trunk/src/series/civ_series.m (revision 1090) @@ -331,6 +331,7 @@ end if CheckInputFile + OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); 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},... + ncfile=fullfile_uvmat(OutputPath,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 @@ -341,12 +342,13 @@ 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),... + ncfile=fullfile_uvmat(OutputPath,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),[],... + ncfile=fullfile_uvmat(OutputPath,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); @@ -409,5 +411,5 @@ end end - if ~exist(ImageName_A,'file') + if isempty(regexp(ImageName_A,'(^http://)|(^https://)')) && ~exist(ImageName_A,'file') disp([ImageName_A ' missing']) continue @@ -425,5 +427,5 @@ FileType_B=FileInfo_B.FileType; end - if ~exist(ImageName_B,'file') + if isempty(regexp(ImageName_B,'(^http://)|(^https://)')) && ~exist(ImageName_B,'file') disp([ImageName_B ' missing']) continue @@ -492,5 +494,5 @@ par_civ1.Mask=mask; %use mask already opened else - if exist(maskname,'file') + if ~isempty(regexp(maskname,'(^http://)|(^https://)'))|| exist(maskname,'file') try par_civ1.Mask=imread(maskname);%update the mask, an store it for future use Index: trunk/src/series/merge_proj.m =================================================================== --- trunk/src/series/merge_proj.m (revision 1089) +++ trunk/src/series/merge_proj.m (revision 1090) @@ -252,4 +252,5 @@ CheckOverwrite=Param.CheckOverwrite; end +OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); for index=1:NbField update_waitbar(WaitbarHandle,index/NbField) @@ -276,5 +277,5 @@ end end - OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1,i2,j1,j2); + OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1,i2,j1,j2); if ~CheckOverwrite && exist(OutputFile,'file') disp(['existing output file ' OutputFile ' already exists, skip to next field']) Index: trunk/src/series/sliding_average.m =================================================================== --- trunk/src/series/sliding_average.m (revision 1090) +++ trunk/src/series/sliding_average.m (revision 1090) @@ -0,0 +1,277 @@ +%'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 2008-2020, 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 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='.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) +if isfield(Param,'InputFields') + InputFields{1}=Param.InputFields; +end + +nbfiles=0; +nbmissing=0; + +%% initialisation +T=24.2; %main wave period +NbPeriod=2; %number of periods for the sliding average +omega=2*pi/T; + +DataOut.ListGlobalAttribute= {'Conventions','Time'}; +DataOut.Conventions='uvmat'; +DataOut.ListVarName={'coord_y','coord_x','Umean','Vmean','Ucos','Vcos','DUDXsin','DUDYsin','DVDXsin','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'}}; + +%%%%%%%%%%%%%%%% 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) + +%%%%%%%%%%%%%%%% 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,errormsg] = 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; + DataOut.coord_y=Field.coord_y; + 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); + DUDXsin=zeros(NpTime,npy,npx); + DUDYsin=zeros(NpTime,npy,npx); + DVDXsin=zeros(NpTime,npy,npx); + DVDYsin=zeros(NpTime,npy,npx); + end + Time(index)=Field.Time; + 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 + DUDXsin=circshift(DUDXsin,[-1 0 0]); + DUDYsin=circshift(DUDYsin,[-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)); + DUDXsin(end,:,:)=Field.DUDX*sin(omega*Time(index)); + DUDYsin(end,:,:)=Field.DUDY*sin(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; + DataOut.Umean=squeeze(nanmean(Umean,1)); + DataOut.Vmean=squeeze(nanmean(Vmean,1)); + DataOut.Ucos=2*squeeze(nanmean(Ucos,1)); + DataOut.Vcos=2*squeeze(nanmean(Vcos,1)); + DataOut.DUDXsin=2*squeeze(nanmean(DUDXsin,1)); + DataOut.DUDYsin=2*squeeze(nanmean(DUDYsin,1)); + DataOut.DVDXsin=2*squeeze(nanmean(DVDXsin,1)); + DataOut.DVDYsin=2*squeeze(nanmean(DVDYsin,1)); + DataOut.Ustokes=(1/omega)*(DataOut.Ucos.*DataOut.DUDXsin+DataOut.Vcos.*DataOut.DUDYsin); + DataOut.Vstokes=(1/omega)*(DataOut.Ucos.*DataOut.DVDXsin+DataOut.Vcos.*DataOut.DVDYsin); + % writing the result file as netcdf file + if index-round(NpTime/2)>=1 + OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomType{1},index-round(NpTime/2)); + %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 + end +end +%%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% +