%'time_series': extract a time series, used with series.fig % 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 %%%%%%%%%%%%%%%%%%%%%%%%%%% % % This function is used in four modes by the GUI series: % 1) config GUI: with no input argument, the function determine the suitable GUI configuration % 2) interactive input: the function is used to interactively introduce input parameters, and then stops % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. % % This function is used in four modes by the GUI series: % 1) config GUI: with no input argument, the function determine the suitable GUI configuration % 2) interactive input: the function is used to interactively introduce input parameters, and then stops % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. % %OUTPUT % GUI_input=list of 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 % In the absence of input (as activated when the current Action is selected % in series), the function ouput GUI_input 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 % .OutputDir: directory for data outputs, including path % .Action: .ActionName: name of the current activated function % .ActionPath: path of the current activated function % .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 % .TransformHandle: corresponding function handle % .InputFields: sub structure describing the input fields withfields % .FieldName: name 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 % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % function ParamOut=time_series(Param) %% set the input elements needed on the GUI series when the action is selected in the menu ActionName if ~exist('Param','var') % case with no input parameter ParamOut={'NbViewMax';2;...% max nbre of input file series (default='' , no limitation) 'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default) 'WholeIndexRange';'off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) 'NbSlice';'on'; ...%nbre of slices ('off' by default) 'VelType';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) 'FieldName';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) 'FieldTransform'; 'on';...%can use a transform function 'ProjObject';'on';...%can use projection object(option 'off'/'on', 'Mask';'off';...%can use mask option (option 'off'/'on', 'off' by default) 'OutputDirExt';'.tseries';...%set the output dir extension ''}; return end %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% %% select different modes, RUN, parameter input, BATCH % BATCH case: read the xml file for batch case if ischar(Param) Param=xml2struct(Param); checkrun=0; % RUN case: parameters introduced as the input structure Param else hseries=guidata(Param.hseries);%handles of the GUI series WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series if isfield(Param,'Specific')&& strcmp(Param.Specific,'?') checkrun=1;% will only search interactive input parameters (preparation of BATCH mode) else checkrun=2; % indicate the RUN option is used end end ParamOut=Param; %default output %% root input file(s) and type RootPath=Param.InputTable(:,1); RootFile=Param.InputTable(:,3); SubDir=Param.InputTable(:,2); NomType=Param.InputTable(:,4); FileExt=Param.InputTable(:,5); % get the set of input file names (cell array filecell), and the lists of % input file or frame indices i1_series,i2_series,j1_series,j2_series [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); % filecell{iview,fileindex}: cell array representing the list of file names % 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 % set of frame indices used for movie or multimage input % numbers of slices and file indices NbSlice=1;%default if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) NbSlice=Param.IndexRange.NbSlice; end 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 nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) nbfield=nbfield_i*NbSlice; %total number of fields after adjustement %determine the file type on each line from the first input file ImageTypeOptions={'image','multimage','mmreader','video'}; 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 [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); 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 mode=''; %default timecell={}; itime=0; NbSlice_calib={}; XmlData=cell(1,nbview);%initiate the structures containing the data from the xml file (calibration and timing) for iview=1:nbview%Loop on views SubDirBase=regexprep(SubDir{iview},'\..*','');%take the root part of SubDir, before the first dot '.' filexml=[fullfile(RootPath{iview},SubDirBase) '.xml'];%new convention: xml at the level of the image folder if ~exist(filexml,'file') filexml=[fullfile(RootPath{iview},SubDir{iview},RootFile{iview}) '.xml']; % old convention: xml inside the image folder if ~exist(filexml,'file') filexml=[fullfile(RootPath{iview},SubDir{iview},RootFile{iview}) '.civ']; % very old convention: .civ file if ~exist(filexml,'file') filexml=''; end end end if ~isempty(filexml) [XmlData{iview},error]=imadoc2struct(filexml); end if isfield(XmlData{iview},'Time') itime=itime+1; timecell{itime}=XmlData{iview}.Time; end if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); end end end %% check coincidence in time for several input file series multitime=0; if isempty(timecell) time=[]; elseif length(timecell)==1 time=timecell{1}; elseif length(timecell)>1 multitime=1; for icell=1:length(timecell) if ~isequal(size(timecell{icell}),size(timecell{1})) msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') time=timecell{1}; multitime=0; break end end end if multitime for icell=1:length(timecell) time(icell,:,:)=timecell{icell}; end diff_time=max(max(diff(time))); if diff_time>0 msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) end end if size(time,2) < i2_series{1}(end) ||( ~isempty(j2_series{1}) && size(time,3) < j2_series{1}(end))% time array absent or too short in ImaDoc xml file' time=[]; end %% coordinate transform or other user defined transform transform_fct='';%default if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'TransformHandle') transform_fct=Param.FieldTransform.TransformHandle; 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 if nbview==2 && ~isequal(CheckImage{1},CheckImage{2}) msgbox_uvmat('ERROR','input must be two image series or two netcdf file series') return end NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series if NbSlice~=nbfield_j answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]); if ~strcmp(answer,'Yes') return end end %% Set field names and velocity types InputFields{1}=[];%default (case of images) if isfield(Param,'InputFields') InputFields{1}=Param.InputFields; end if nbview==2 InputFields{2}=[];%default (case of images) if isfield(Param,'InputFields') InputFields{2}=Param.InputFields{1};%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 %%% TO UPDATE if isequal(InputFields{1},'get_field...') hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI if numel(hget_field)>1 delete(hget_field(2:end)) % delete multiple occurerence of the GUI get_fioeld elseif isempty(hget_field) filename=filecell{1,1}; % filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),num_j2{1}(1),SubDir{1}); idetect(iview)=exist(filename,'file'); hget_field=get_field(filename); return end SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI if isempty(SubField) delete(hget_field) filename=filecell{1,1}; %filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),j2_series{1}(1),SubDir{1}); hget_field=get_field(filename); SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI 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) msgbox_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg]) 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 %% LOOP ON SLICES nbmissing=0; %number of undetected files for i_slice=1:NbSlice dt=[]; %%%%%%%%%%%%%%%%%%%%%%%%%%%% LOOP ON FIELDS WITHIN A SLICE filecounter=0; for ifile=i_slice:NbSlice:nbfield if checkrun update_waitbar(hseries.waitbar_frame,WaitbarPos,ifile/nbfield) stopstate=get(hseries.RUN,'BusyAction'); else stopstate='queue'; end errormsg=''; if isequal(stopstate,'queue')% enable STOP command % loop on views (in case of multiple input series) for iview=1:nbview filename=filecell{iview,ifile}; % filename=name_generator(filebase{iview},... % i1_series{iview}(ifile),j1_series{iview}(ifile),FileExt{iview},NomType{iview},1,i2_series{iview}(ifile),j2_series{iview}(ifile),SubDir{iview}); if exist(filename,'file') try Data{iview}=[]; %default if ~isequal(FileType{iview},'netcdf') Data{iview}.ListVarName={'A'}; Data{iview}.AName='image'; switch FileType{iview} case 'movie' A=read(MovieObject{iview},i1_series{iview}(ifile)); case 'avi' mov=aviread(filename,i1_series{iview}(ifile)); A=frame2im(mov(1)); case 'vol' A=imread(filename); case 'multimage' A=imread(filename,i1_series{iview}(ifile)); case 'image' A=imread(filename); end Data{iview}.ListVarName={'AY','AX','A'}; % npy=size(A,1); npx=size(A,2); nbcolor=size(A,3); if nbcolor==3 Data{iview}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; else Data{iview}.VarDimName={'AY','AX',{'AY','AX'}}; end Data{iview}.AY=[npy-0.5 0.5]; Data{iview}.AX=[0.5 npx-0.5]; Data{iview}.A=double(A); Data{iview}.CoordUnit='pixel'; elseif testcivx [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); if ~isequal(FieldName,{''}) Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..) end else [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data Data{iview}.VarAttribute=SubField.VarAttribute; end if ~isempty(NbSlice_calib) % z index Data{iview}.ZIndex=mod(i1_series{iview}(ifile)-1,NbSlice_calib{1})+1; end catch ME errormsg=ME.message; end else errormsg=[filename ' is missing']; end if isempty(errormsg) % coordinate transform (or other user defined transform) if ~isempty(transform_fct) if nbview==2 [Data{1},Data{2}]=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); if isempty(Data{2}) Data(2)=[]; end else Data{1}=transform_fct(Data{1},XmlData{1}); end end if length(Data)==2 [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields else Field=Data{1}; end if Param.CheckObject [Field,errormsg]=proj_field(Field,Param.ProjObject); end end filecounter=filecounter+1; % initiate the time series at the first iteration if filecounter==1 % stop program if the first field reading is in error if ~isempty(errormsg) msgbox_uvmat('ERROR',['error in time_series/sub_field:' errormsg]) return end DataOut=Field;%default DataOut.NbDim=Field.NbDim+1; %add the time dimension for plots nbvar=length(Field.ListVarName); if nbvar==0 msgbox_uvmat('ERROR','no input variable selected in get_field') return end 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') msgbox_uvmat('ERROR','do not handle error flags in time series') return end if isequal(var_role,'warnflag') testsum(ivar)=0; % not recorded variable eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable end if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|... isequal(var_role,'coord_z')|isequal(var_role,'coord') testsum(ivar)=1; %constant coordinates, record without time evolution 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 eval(['DataOut.' Field.ListVarName{ivar} '=[];']) end end DataOut.ListVarName=[{'Time'} DataOut.ListVarName]; end % add data to the current field for ivar=1:length(Field.ListVarName) VarName=Field.ListVarName{ivar}; VarVal=Field.(VarName); if testsum(ivar)==2% test for recorded variable if isempty(errormsg) if isequal(Param.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode if isempty(VarVal) msgbox_uvmat('ERROR',['empty result at frame index ' num2str(i1_series{iview}(ifile))]) return end VarVal=mean(VarVal,1); end VarVal=shiftdim(VarVal,-1); %shift dimension DataOut.(VarName)=cat(1,DataOut.(VarName),VarVal);%concanete the current field to the time series else DataOut.(VarName)=cat(1,DataOut.(VarName),0);% put each variable to 0 in case of input reading error end elseif testsum(ivar)==1% variable representing fixed coordinates eval(['VarInit=DataOut.' VarName ';']); if isempty(errormsg) && ~isequal(VarVal,VarInit) msgbox_uvmat('ERROR',['time series requires constant coordinates ' VarName]) return end end end % record the time: if isempty(time)% time read in ncfiles if isfield(Field,'Time') DataOut.Time(filecounter,1)=Field.Time; else DataOut.Time(filecounter,1)=ifile;%default end else % time from ImaDoc prevails TODO: correct % DataOut.Time(filecounter,1)=time{1}(i1_series{1})(ifile),j1_series{1}(ifile))+time(end,i2_series{end}(ifile),j2_series{end}(ifile)))/2; DataOut.Time(filecounter,1)=i1_series{1}(ifile);% TODO : generalise end % record the number of missing input fields if ~isempty(errormsg) nbmissing=nbmissing+1; display(['ifile=' num2str(ifile) ':' errormsg]) end end 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 testsum(ivar)==2%variable used as time series DataOut.VarDimName{ivar}=[{'Time'} DimCell]; elseif testsum(ivar)==1 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:filecounter]; end % display nbmissing if ~isequal(nbmissing,0) msgbox_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display']) end %name of result file % filemean=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},'.nc','_1',i1_series{1}(i_slice)); OutputFile=fullfile_uvmat(RootPath{1},Param.OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),i_slice,[]); errormsg=struct2nc(OutputFile,DataOut); %save result file if isempty(errormsg) display([OutputFile ' written']) else msgbox_uvmat('ERROR',['error in Series/struct2nc: ' errormsg]) end end %% plot the time series (the last one in case of multislices) 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)