%'time_series': extract a time series after projection on an object (points , line..) % this function can be used as a template for applying a global operation on a series of input fields %------------------------------------------------------------------------ % function GUI_input=time_series(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=time_series(Param) %% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN 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 = {'phys','phys_polar'};%can use a transform function, proposed list (needed for compilation) ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) if 1==2 % loop used to enforce compilation of transform fct, never entered. phys phys_polar end 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='.tseries';%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 % check for selection of a projection object hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series 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 end % introduce bin size for histograms if isfield(Param,'CheckObject') &&Param.CheckObject SeriesData=get(hseries,'UserData'); if ismember(SeriesData.ProjObject.ProjMode,{'inside','outside'}) answer=msgbox_uvmat('INPUT_TXT','set bin size for histograms (or keep ''auto'' by default)?','auto'); ParamOut.ActionInput.VarMesh=str2num(answer); end end % test for subtraction if size(Param.InputTable,1)>2 msgbox_uvmat('WARNING','''time_series'' uses only one or two input lines (two for substraction). To concatene fields first use ''merge_proj'''); end if size(Param.InputTable,1)>=2 answer=msgbox_uvmat('INPUT_Y-N','substract the two input file series?'); if strcmp(answer,'Yes') if isempty(Param.FieldTransform.TransformName) set(hhseries.TransformName,'value',2) %select sub_field end else set(hhseries.InputTable,'Data',Param.InputTable(1,:)) end end % check the existence of the first and last file in the series first_j=[]; if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end last_j=[]; if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end PairString=''; if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); if ~exist(FirstFileName,'file') msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) else [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); if ~exist(LastFileName,'file') msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) end 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); hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); % gives the series of input file names and indices set by the input parameters: [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); % filecell{iview,fileindex}: % iview: line in the table corresponding to a given file series % fileindex: file index with i and j reshaped as a 1D array % 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 if ~isempty(hdisp),delete(hdisp),end;%end the waiting display 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'}; FileType=cell(1,NbView); FileInfo=cell(1,NbView); MovieObject=cell(1,NbView); CheckImage=cell(1,NbView); CheckNc=cell(1,NbView); frame_index=cell(1,NbView); for iview=1:NbView if ~exist(filecell{iview,1}','file') disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) return end [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); FileType{iview}=FileInfo{iview}.FileType; if strcmp(FileType{iview},'civdata')||strcmp(FileType{iview},'civx') if ~isfield(Param.InputFields,'VelType') FileType{iview}='netcdf';% civ data read as usual netcdf files end end 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}=i1_series{iview}; else frame_index{iview}=j1_series{iview}; end 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 ~isempty(errormsg) disp_uvmat('ERROR',['error in reading xmlfile: ' errormsg],checkrun) return end if size(time,1)>1 diff_time=max(max(diff(time))); if diff_time>0 disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) end time=time(1,:);% choose the time data from the first sequence 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) if isfield(Param,'TransformInput') XmlData{1}.TransformInput=Param.TransformInput; end end %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% % EDIT FROM HERE %% check the validity of the input file types if ~CheckImage{1}&&~CheckNc{1} disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun) return end if NbView==2 && ~isequal(CheckImage{1},CheckImage{2}) disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun) return end %% settings for the output file FileExtOut='.nc';% write result as .nc files for netcdf inputs 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 NbView==2 InputFields{2}=[];%default (case of images) end if isfield(Param,'InputFields') InputFields{1}=Param.InputFields; if NbView==2 InputFields{2}=Param.InputFields;%default if isfield(Param.InputFields,'FieldName_1') InputFields{2}.FieldName=Param.InputFields.FieldName_1; if isfield(Param.InputFields,'VelType_1') InputFields{2}.VelType=Param.InputFields.VelType_1; end end end end %% Initiate output fields %initiate the output structure as a copy of the first input one (reproduce fields) [DataOut,tild,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1); if ~isempty(errormsg) disp_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg],checkrun) return end time_1=[]; if isfield(DataOut,'Time') time_1=DataOut.Time(1); end if CheckNc{iview} if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute)) DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute]; end DataOut.Conventions='uvmat'; DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}]; ActionKey='Action'; while isfield(DataOut,ActionKey) ActionKey=[ActionKey '_1']; end DataOut.(ActionKey)=Param.Action; DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}]; if isfield(DataOut,'Time') DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}]; end end nbfile=0;% not used , to check nbmissing=0; VarMesh=[]; checkhisto=0; checkline=0; if isfield(Param,'ProjObject') if ismember(Param.ProjObject.ProjMode,{'inside','outside'}) checkhisto=1; if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms VarMesh=Param.ActionInput.VarMesh; else VarMesh=[]; disp_uvmat('WARNING','automatic bin size for histograms, select time_series again to set the value',checkrun) end elseif ismember(Param.ProjObject.Type,{'line'}) checkline=1; end end %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% for index=1:NbField update_waitbar(WaitbarHandle,index/NbField) if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') break % leave the loop if stop is ordered end Data=cell(1,NbView);%initiate the set Data; nbtime=0; dt=[]; %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% for iview=1:NbView % reading input file(s) [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); if ~isempty(errormsg) errormsg=['time_series / read_field / ' errormsg]; disp(errormsg) break% exit the loop on iview end if ~isempty(NbSlice_calib) Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform end end if ~isempty(errormsg) continue %in case of input error skip the current input field, go to next index end Field=Data{1}; % default input field structure % coordinate transform (or other user defined transform) if ~isempty(transform_fct) switch nargin(transform_fct) case 4 if length(Data)==2 Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); else Field=transform_fct(Data{1},XmlData{1}); end case 3 if length(Data)==2 Field=transform_fct(Data{1},XmlData{1},Data{2}); else Field=transform_fct(Data{1},XmlData{1}); end case 2 Field=transform_fct(Data{1},XmlData{1}); case 1 Field=transform_fct(Data{1}); end end %field projection on an object if Param.CheckObject % calculate tps coefficients if needed if isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps') Field=tps_coeff_field(Field,check_proj_tps); end [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh); if ~isempty(errormsg) disp_uvmat('ERROR',['time_series / proj_field / ' errormsg],checkrun) return end end % nbfile=nbfile+1; % initiate the time series at the first iteration if index==1 % stop program if the first field reading is in error if ~isempty(errormsg) disp_uvmat('ERROR',['time_series / sub_field / ' errormsg],checkrun) return end if ~isfield(Field,'ListVarName') disp_uvmat('ERROR','no variable in the projected field',checkrun) return end DataOut=Field;%output reproduced the first projected field by default nbvar=length(Field.ListVarName); if nbvar==0 disp_uvmat('ERROR','no input variable selected',checkrun) return end if checkhisto%case of histograms testsum=zeros(1,nbvar);%initiate flag for action on each variable for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram) VarName=Field.ListVarName{ivar}; if isfield(Data{1},VarName) DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Histo']}]; DataOut.VarDimName=[DataOut.VarDimName {{'Time',VarName}}]; StatName=pdf2stat;% get the names of statistical quantities to calcuilate at each time for istat=1:numel(StatName) DataOut.ListVarName=[DataOut.ListVarName {[VarName StatName{istat}]}]; DataOut.VarDimName=[DataOut.VarDimName {'Time'}]; end testsum(ivar)=1; DataOut.(VarName)=Field.(VarName); DataOut.([VarName 'Histo'])=zeros([NbField numel(DataOut.(VarName))]); VarMesh=Field.(VarName)(2)-Field.(VarName)(1); end end disp(['mesh for histogram = ' num2str(VarMesh)]) else testsum=2*ones(1,nbvar);%initiate flag for action on each variable if isfield(Field,'VarAttribute') % look for coordinate and flag variables for ivar=1:nbvar if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role') var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable if isequal(var_role,'errorflag') disp_uvmat('ERROR','do not handle error flags in time series',checkrun) return end if isequal(var_role,'warnflag') testsum(ivar)=0; % not recorded variable eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable end if strcmp(var_role,'coord_x')||strcmp(var_role,'coord_z')||strcmp(var_role,'coord') testsum(ivar)=1; %constant coordinates, record without time evolution end if strcmp(var_role,'coord_y')&& ~checkline testsum(ivar)=1; end end % check whether the variable ivar is a dimension variable DimCell=Field.VarDimName{ivar}; if ischar(DimCell) DimCell={DimCell}; end if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables testsum(ivar)=1; end end end for ivar=1:nbvar if testsum(ivar)==2 VarName=Field.ListVarName{ivar}; siz=size(Field.(VarName)); DataOut.(VarName)=zeros([NbField siz]); end end end DataOut.ListVarName=[{'Time'} DataOut.ListVarName]; end % end initialisation for index==1 % append data from the current field if checkhisto % case of histogram (projection mode=inside or outside) for ivar=1:length(Field.ListVarName) VarName=Field.ListVarName{ivar}; if isfield(Data{1},VarName) MaxValue=max(DataOut.(VarName));% current max of histogram absissa MinValue=min(DataOut.(VarName));% current min of histogram absissa MaxIndex=round(MaxValue/VarMesh); MinIndex=round(MinValue/VarMesh); MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field MinIndex_new=round(min(Field.(VarName)/VarMesh)); if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(NbField,MaxIndex_new-MaxIndex)]; % append the new histo values end if MinIndex_new <= MinIndex-1 DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values DataOut.([VarName 'Histo'])=[zeros(NbField,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values ind_start=1; else ind_start=MinIndex_new-MinIndex+1; end DataOut.([VarName 'Histo'])(index,ind_start:ind_start+MaxIndex_new-MinIndex_new)=... DataOut.([VarName 'Histo'])(index,ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']); VarVal=pdf2stat((Field.(VarName))',(Field.([VarName 'Histo']))');% max of the current field for istat=1:numel(VarVal) DataOut.([VarName StatName{istat}])(index)=VarVal(istat); end end end else % not histogram for ivar=1:length(Field.ListVarName) VarName=Field.ListVarName{ivar}; VarVal=Field.(VarName); if testsum(ivar)==2% test for recorded variable if isempty(errormsg) VarVal=shiftdim(VarVal,-1); %shift dimension DataOut.(VarName)(index,:,:)=VarVal;%concanete the current field to the time series end elseif testsum(ivar)==1% variable representing fixed coordinates VarInit=DataOut.(VarName); if isempty(errormsg) && ~isequal(VarVal,VarInit) disp_uvmat('ERROR',['time series requires constant coordinates ' VarName ': use projection mode interp'],checkrun) return end end end end % record the time: if isempty(time)% time not set by xml filer(s) if isfield(Data{1},'Time') DataOut.Time(index,1)=Field.Time; else DataOut.Time(index,1)=index;%default end else % time from ImaDoc prevails TODO: correct DataOut.Time(index,1)=time(index);% end index % record the number of missing input fields if ~isempty(errormsg) nbmissing=nbmissing+1; display(['index=' num2str(index) ':' errormsg]) end end %%%%%%% END OF LOOP WITHIN A SLICE %remove time for global attributes if exists Time_index=find(strcmp('Time',DataOut.ListGlobalAttribute)); if ~isempty(Time_index) DataOut.ListGlobalAttribute(Time_index)=[]; end DataOut.Conventions='uvmat'; for ivar=1:numel(DataOut.ListVarName) VarName=DataOut.ListVarName{ivar}; eval(['DataOut.' VarName '=squeeze(DataOut.' VarName ');']) %remove singletons end % add time dimension for ivar=1:length(Field.ListVarName) DimCell=Field.VarDimName{ivar}; if ischar(DimCell),DimCell={DimCell};end if testsum(ivar)==2% variable for which time series is calculated DataOut.VarDimName{ivar}=[{'Time'} DimCell]; elseif testsum(ivar)==1 % variable represneting a fixed coordinate DataOut.VarDimName{ivar}=DimCell; end end indexremove=find(~testsum); if ~isempty(indexremove) DataOut.ListVarName(1+indexremove)=[]; DataOut.VarDimName(indexremove)=[]; if isfield(DataOut,'Role') && ~isempty(DataOut.Role{1})%generaliser aus autres attributs DataOut.Role(1+indexremove)=[]; end end %shift variable attributes if isfield(DataOut,'VarAttribute') DataOut.VarAttribute=[{[]} DataOut.VarAttribute]; end DataOut.VarDimName=[{'Time'} DataOut.VarDimName]; DataOut.Action=Param.Action;%name of the processing programme test_time=diff(DataOut.Time)>0;% test that the readed time is increasing (not constant) if ~test_time DataOut.Time=1:NbField; end if ~isequal(nbmissing,0) disp_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'],checkrun) end %% name of result file OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); errormsg=struct2nc(OutputFile,DataOut); %save result file if isempty(errormsg) display([OutputFile ' written']) else disp_uvmat('ERROR',['error in Series/struct2nc: ' errormsg],checkrun) end %% plot the time series for (the last one in case of multislices) if checkrun %&& isfield(Param,'ProjObject') && strcmp(Param.ProjObject.Type,'points') %% open the result file with uvmat (in RUN mode) uvmat(OutputFile)% open the last result file with uvmat end % figure % haxes=axes; % plot_field(DataOut,haxes) % % %% display the result file using the GUI get_field % hget_field=findobj(allchild(0),'name','get_field'); % if ~isempty(hget_field) % delete(hget_field) % end % get_field(OutputFile,DataOut) % end