Index: /trunk/src/find_field_cells.m =================================================================== --- /trunk/src/find_field_cells.m (revision 1084) +++ /trunk/src/find_field_cells.m (revision 1085) @@ -155,5 +155,5 @@ for iscalar=1:numel(ind_scalar) icell=[]; - for iprev=1:numel(DimCell)-1 + for iprev=1:numel(DimCell) if isequal(DimCell{iprev},Data.VarDimName{ind_scalar(iscalar)}) icell=iprev; Index: /trunk/src/phys_ima.m =================================================================== --- /trunk/src/phys_ima.m (revision 1084) +++ /trunk/src/phys_ima.m (revision 1085) @@ -66,5 +66,5 @@ % the image needs to be interpolated to the new coordinates Z=0; %default - if isfield(Calib,'SliceCoord') %.Z= index of plane + if isfield(Calib,'SliceCoord')&& size(Calib.SliceCoord,1)>=ZIndex %.Z= index of plane SliceCoord=Calib.SliceCoord(ZIndex,:); Z=SliceCoord(3); Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 1084) +++ /trunk/src/proj_field.m (revision 1085) @@ -672,5 +672,5 @@ %identify error flag errorflag=0; %default, no error flag - if isfield(CellInfo{icell},'VarIndex_errorflag');% test for error flag + if isfield(CellInfo{icell},'VarIndex_errorflag')% test for error flag FFName=FieldData.ListVarName{CellInfo{icell}.VarIndex_errorflag}; errorflag=FieldData.(FFName); Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1084) +++ /trunk/src/series.m (revision 1085) @@ -2093,5 +2093,6 @@ % create file containing the list of jobs ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables - fid=fopen(ListProcess,'w'); % open it for writting + [fid,errormsg]=fopen(ListProcess,'w'); % open it for writting + if isempty(errormsg) for iprocess=1:length(batch_file_list) fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files @@ -2099,5 +2100,7 @@ fclose(fid); system(['chmod +x ' ListProcess]); % set the file to executable - + else + errormsg=['error for writting the executable file:' errormsg]; + end CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes) LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn; Index: /trunk/src/series/aver_spectral.m =================================================================== --- /trunk/src/series/aver_spectral.m (revision 1085) +++ /trunk/src/series/aver_spectral.m (revision 1085) @@ -0,0 +1,245 @@ +%'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 2008-2020, 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=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_multi';%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={''}; + 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 + +main_period=Param.ActionInput.WavePeriod; +main_frequency=2*pi/main_period; +frequency=(0:main_frequency/16:3*main_frequency)'; +nbfrequency=numel(frequency); +%%%%%%%%%%%%%%%% 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 + %initiate average + if index==1 + nby=numel(Data.coord_y); + nbx=numel(Data.coord_x); + cos_U=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); + sin_U=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); + cos_V=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); + sin_V=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); + NbField=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); + end + %update average + FF=isnan(Data.U)|isnan(Data.V);% check NaN values + Data.U(FF)=0;% set to zero the NaN values + Data.V(FF)=0; + for ifreq=1:nbfrequency + NbField(ifreq,:,:)=NbField(ifreq,:,:)+reshape(~FF,1,nby,nbx);%count the NaN values + cos_U(ifreq,:,:)=cos_U(ifreq,:,:)+reshape(Data.U,1,nby,nbx)*cos(Data.Time*frequency(ifreq)); + sin_U(ifreq,:,:)=sin_U(ifreq,:,:)+reshape(Data.U,1,nby,nbx)*sin(Data.Time*frequency(ifreq)); + cos_V(ifreq,:,:)=cos_V(ifreq,:,:)+reshape(Data.V,1,nby,nbx)*cos(Data.Time*frequency(ifreq)); + sin_V(ifreq,:,:)=sin_V(ifreq,:,:)+reshape(Data.V,1,nby,nbx)*sin(Data.Time*frequency(ifreq)); + end +end + +%%%%%%%%%%%%%%%%%%%%%%%% +Data.ListVarName={'coord_x','coord_y','frequency','cos_U','cos_V','sin_U','sin_V','a_U','a_V','phase_U','phase_V'}; +%Data.ListVarName=[{'coord_y','coord_x'} Data.ListVarName]; +Data.VarDimName={'coord_x', 'coord_y','frequency'}; +for ilist=1:numel(Data.ListVarName)-3 + Data.VarDimName{ilist+3}={'frequency','coord_y','coord_x'}; +end +Data.frequency=frequency; +Data.cos_U=cos_U./NbField; +Data.sin_U=sin_U./NbField; +Data.cos_V=cos_V./NbField; +Data.sin_V=sin_V./NbField; +Data.a_U=sqrt(2)*sqrt(Data.cos_U.*Data.cos_U+Data.sin_U.*Data.sin_U); +Data.a_V=sqrt(2)*sqrt(Data.cos_V.*Data.cos_V+Data.sin_V.*Data.sin_V); +Data.phase_U=angle(Data.cos_U+1i*Data.sin_U); +Data.phase_V=angle(Data.cos_V+1i*Data.sin_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 ####' Index: /trunk/src/series/time_series.m =================================================================== --- /trunk/src/series/time_series.m (revision 1084) +++ /trunk/src/series/time_series.m (revision 1085) @@ -81,10 +81,5 @@ hhseries=guidata(hseries); if ~isfield(Param,'ProjObject') - answer=msgbox_uvmat('INPUT_Y-N','use a projection object for the time_series?'); - if strcmp(answer,'Yes') - set(hhseries.CheckObject,'Visible','on') - set(hhseries.CheckObject,'Value',1) - series('CheckObject_Callback',hseries,[],hhseries); %file input with xml reading in uvmat, show the image in phys coordinates - end + msgbox_uvmat('WARNING','you may need to introduce a projection object for the time_series'); end