function GUI_input=time_series(num_i1,num_i2,num_j1,num_j2,Series) %---------------------------------------------------------------------- % --- make a time series analysis %---------------------------------------------------------------------- %INPUT: %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) %OTHER INPUTS given by the structure Series %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) if ~exist('num_i1','var') GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) 'RootFile';'on';... %root input file name ('on' by default) 'FileExt';'on';... %input file extension ('on' by default) 'NomType';'on';...%type of file indexing ('on' by default) 'NbSlice';'on'; ...%nbre of slices ('off' by default) 'VelTypeMenu';'two';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) 'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) 'CoordType';'on';...%can use a transform function 'off' by default 'GetObject';'on';...%can use projection object ,'off' by default %'GetMask';'on'...%can use mask option ,'off' by default %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter ''}; return %exit the function end %------------------------------------------------------ hseries=guidata(Series.hseries);%handles in the GUI series WaitbarPos=get(hseries.waitbar_frame,'Position'); %position of the waitbar frame %projection object test_object=get(hseries.GetObject,'Value'); if test_object hset_object=findobj(allchild(0),'Name','set_object'); ProjObject=read_set_object(guidata(hset_object)); %answeryes=questdlg({['field series projected on ' Series.ProjObject.Style]}); answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Style]); if ~isequal(answeryes,'Yes') return end else msgbox_uvmat('ERROR','a projection object is needed'); return end % root names if iscell(Series.RootPath) RootPath=Series.RootPath; RootFile=Series.RootFile; SubDir=Series.SubDir; FileExt=Series.FileExt; NomType=Series.NomType; else RootPath={Series.RootPath}; RootFile={Series.RootFile}; SubDir={Series.SubDir}; FileExt={Series.FileExt}; NomType={Series.NomType}; num_i1={num_i1}; num_i2={num_i2}; num_j1={num_j1}; num_j2={num_j2}; end ext=FileExt{1}; form=imformats(ext([2:end]));%test valid Matlab image formats testima=0; if ~isempty(form)||isequal(lower(ext),'.avi') testima=1; end nbview=length(RootPath);%number of series (1 or 2) nbfield=size(num_i1{1},1)*size(num_i1{1},2); %number of fields in the time series %Number of input series: this function accepts only a single input file series nbview=length(RootPath); if nbview==2 %TODO: choose between difference and two series elseif nbview>2 % TODO: make multiple series % RootPath=RootPath(1:2); % set(hseries.RootPath,'String',RootPath) % SubDir=SubDir(1:2); % set(hseries.SubDir,'String',SubDir) % RootFile=RootFile(1:2); % set(hseries.RootFile,'String',RootFile) % NomType=NomType(1:2); % %set(hseries.NomType,'String',NomType) % FileExt=FileExt(1:2); % set(hseries.FileExt,'String',FileExt) % nbview=2; end %determine image type hhh=which('mmreader'); for iview=1:nbview if isequal(FileExt{iview},'.nc')||isequal(FileExt{iview},'.cdf') FileType{iview}='netcdf'; elseif isequal(lower(FileExt{iview}),'.avi') if ~isequal(hhh,'')&& mmreader.isPlatformSupported() MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); FileType{iview}='movie'; else FileType{iview}='avi'; end elseif isequal(lower(FileExt{iview}),'.vol') FileType{iview}='vol'; else form=imformats(FileExt{iview}(2:end)); if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab if isequal(NomType{iview},'*'); FileType{iview}='multimage'; else FileType{iview}='image'; end end end end filebase{1}=fullfile(RootPath{1},RootFile{1}); % number of slices NbSlice=str2num(get(hseries.NbSlice,'String')); if isempty(NbSlice) NbSlice=1; end NbSlice_name=num2str(NbSlice); % Field and velocity type (the same for the two views) if isfield(Series,'Field') FieldName=Series.Field;%the same set of fields for all views else FieldName={''}; end if isequal(FieldName,{'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=name_generator(filebase{1},num_i1{1}(1),num_j1{1}(1),FileExt{1},NomType{1},1,num_i2{1}(1),num_j2{1}(1),SubDir{1}); idetect(iview)=exist(filename,'file'); hget_field=get_field(filename); return end %hhget_field=guidata(hget_field);%handles of GUI elements in get_field 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=name_generator(filebase{1},num_i1{1}(1),num_j1{1}(1),FileExt{1},NomType{1},1,num_i2{1}(1),num_j2{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 % if isequal(get(hhget_field.menu_coord,'Visible'),'on') % list_transform=get(hhget_field.menu_coord,'String'); % val_list=get(hhget_field.menu_coord,'Value'); % transform=list_transform{val_list}; % end end %detect whether the two files are 'images' or 'netcdf' % testima=0; % testvol=0; testcivx=0; % testnc=0; FileExt=get(hseries.FileExt,'String'); % for iview=1:nbview % ext=FileExt{iview}; % form=imformats(ext([2:end])); % if isequal(lower(ext),'.vol') % testvol=testvol+1; % elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab % testima=testima+1; % elseif isequal(ext,'.nc') % testnc=testnc+1; % end % end % if testvol % msgbox_uvmat('ERROR','volume images not implemented yet') % return % end % if testnc~=nbview && testima~=nbview && testvol~=nbview % msgbox_uvmat('need a set of images or a set of netcdf files with the same fields as input','ERROR') % return % end if ~isequal(FieldName,{'get_field...'}) testcivx=isequal(FileType{1},'netcdf'); end % Root name of output files (TO GENERALISE FOR TWO INPUT SERIES) % filebasesub=fullfile(RootPath{1},RootFile{1}); % if NbSlice==1 % filebase_out=[filebasesub '_time']; % else % filebase_out=[filebasesub '_' NbSlice_name 'mtim']; % increment=num_i1{1}(2)-num_i1{1}(1); % if ~isequal(increment,1) % if an increment is set % answeryes=msgbox_uvmat('INPUT_Y-N',['will take time series in ' num2str(NbSlice) 'slices with increment = ' num2str(increment) '!']); % else % answeryes=msgbox_uvmat('INPUT_Y-N',{['will take time series in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_out ' ...']}); % end % if ~isequal(answeryes,'Yes') % return % end % end VelType_str=get(hseries.VelTypeMenu,'String'); VelType_val=get(hseries.VelTypeMenu,'Value'); VelType{1}=VelType_str{VelType_val}; if nbview==2 VelType_str=get(hseries.VelTypeMenu_1,'String'); VelType_val=get(hseries.VelTypeMenu_1,'Value'); VelType{2}=VelType_str{VelType_val}; end %Calibration data and timing: read the ImaDoc files mode=''; %default timecell={}; XmlData={}; itime=0; NbSlice_calib={}; for iview=1:nbview%Loop on views XmlData{iview}=[];%default filebase{iview}=fullfile(RootPath{iview},RootFile{iview}); if exist([filebase{iview} '.xml'],'file') [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); 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 field series'); end end elseif exist([filebase{iview} '.civ'],'file') [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); itime=itime+1; timecell{itime}=time; XmlData{iview}.Time=time; GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; GeometryCalib.Tx=0; GeometryCalib.Ty=0; GeometryCalib.Tz=1; GeometryCalib.dpx=1; GeometryCalib.dpy=1; GeometryCalib.sx=1; GeometryCalib.Cx=0; GeometryCalib.Cy=0; GeometryCalib.f=1; GeometryCalib.kappa1=0; GeometryCalib.CoordUnit='cm'; XmlData{iview}.GeometryCalib=GeometryCalib; if error==1 msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); end end end %check coincidence in time multitime=0; if length(timecell)==0 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 more than ' num2str(diff_time)]) end end if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' time=[]; end % Root name of output files (TO GENERALISE FOR TWO INPUT SERIES) subdir_result='time_series'; % filebasesub=fullfile(RootPath{1},subdir_result,RootFile{1}); % if isempty(SubDir{1}) % create a subdirectory '/aver_stat' % subdir_result='aver_stat'; % filebasemean=fullfile(RootPath{1},subdir_result); if ~exist(fullfile(RootPath{1},subdir_result),'dir') dircur=pwd; %record current working directory cd(RootPath{1})% goes to the iamge directory [m1,m2,m3]=mkdir(subdir_result); if ~isequal(m2,'') msgbox_uvmat('CONFIRMATION',m2);%error message for directory creation end cd(dircur) %back to the initial working directory end filebase_out=filebase{1}; NomTypeOut=nomtype2pair(NomType{1},num_i2{end}(end)-num_i1{1}(1),num_j2{end}(end)-num_j1{1}(1)); % coordinate transform or other user defined transform transform_fct=[];%default if isfield(Series,'transform_fct') transform_fct=Series.transform_fct; end % to update: VelType_str=get(hseries.VelTypeMenu,'String'); VelType_val=get(hseries.VelTypeMenu,'Value'); VelType{1}=VelType_str{VelType_val}; if nbview==2 VelType_str=get(hseries.VelTypeMenu_1,'String'); VelType_val=get(hseries.VelTypeMenu_1,'Value'); VelType{2}=VelType_str{VelType_val}; end %LOOP ON SLICES for i_slice=1:NbSlice dt=[]; nbmissing=0; %number of undetected files nbfiles=0; %%%%%%%%%%%%%%%%%%%%%%%%%%%%LOOP ON FIELDS IN A SLICE for ifile=i_slice:NbSlice:nbfield stopstate=get(hseries.RUN,'BusyAction'); if isequal(stopstate,'queue')% enable STOP command update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) for iview=1:nbview filename=... name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),FileExt{iview},NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview}); idetect(iview)=exist(filename,'file'); 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},num_i1{iview}(ifile)); case 'avi' mov=aviread(filename,num_i1{iview}(ifile)); A=frame2im(mov(1)); case 'vol' A=imread(filename); case 'multimage' A=imread(filename,num_i1{iview}(ifile)); case 'image' A=imread(filename); end Data{iview}.ListVarName={'coord_y','coord_x','A'}; % npy=size(A,1); npx=size(A,2); nbcolor=size(A,3); if nbcolor==3 Data{iview}.VarDimName={'coord_y','coord_x',{'coord_y','coord_x','rgb'}}; else Data{iview}.VarDimName={'coord_y','coord_x',{'coord_y','coord_x'}}; end Data{iview}.coord_y=[npy-0.5 0.5]; Data{iview}.coord_x=[0.5 npx-0.5]; Data{iview}.A=double(A); Data{iview}.CoordType='px'; elseif testcivx [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); 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(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1; end end % coordinate transform (or other user defined transform) if ~isempty(transform_fct) % z index if ~isempty(NbSlice_calib) Data{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1;%Zindex for phys transform end 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); end end if testcivx Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..) end if length(Data)==2 [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields if ~isempty(errormsg) msgbox_uvmat('ERROR',['error in time_series/sub_field:' errormsg]) return end else Field=Data{1}; end if test_object [Field,errormsg]=proj_field(Field,ProjObject); if ~isempty(errormsg) msgbox_uvmat('ERROR',['error in time_series/proj_field:' errormsg]) return end end if min(idetect)>=1% the input file(s) have been detected nbfiles=nbfiles+1; if nbfiles==1 %first field: initiate the time series RecordData=Field;%default RecordData.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 indexfalse=0; CoordName={}; indexremove=[]; 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(['RecordData=rmfield(RecordData,''' 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 % 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 end for ivar=1:nbvar if testsum(ivar)==2 eval(['RecordData.' Field.ListVarName{ivar} '=[];']) end end RecordData.ListVarName=[{'Time'} RecordData.ListVarName]; end for ivar=1:length(Field.ListVarName) VarName=Field.ListVarName{ivar}; eval(['VarVal=Field.' VarName ';']); if testsum(ivar)==2% test for recorded variable eval(['VarVal=Field.' VarName ';']); if isequal(ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode if isempty(VarVal) msgbox_uvmat('ERROR',['empty result at frame index ' num2str(num_i1{iview}(ifile))]) return end VarVal=mean(VarVal,1); end VarVal=shiftdim(VarVal,-1); %shift dimension eval(['RecordData.' VarName '=cat(1,RecordData.' VarName ',VarVal);']);%concanete the current field to the time series elseif testsum(ivar)==1% variable representing fixed coordinates eval(['VarInit=RecordData.' VarName ';']); if ~isequal(VarVal,VarInit) msgbox_uvmat('ERROR',['time series requires constant coordinates ' VarName]) return end end end % time: if isempty(time)% time read in ncfiles if isfield(Field,'Time') RecordData.Time(nbfiles,1)=Field.Time; else RecordData.Time(nbfiles,1)=nbfiles;%default end else % time from ImaDoc prevails RecordData.Time(nbfiles,1)=(time(1,num_i1{1}(ifile),num_j1{1}(ifile))+time(end,num_i2{end}(ifile),num_j2{end}(ifile)))/2; end else nbmissing=nbmissing+1; end end end %remove time for global attributes if exists for iattr=1:numel(RecordData.ListGlobalAttribute) if strcmp(RecordData.ListGlobalAttribute{iattr},'Time') RecordData.ListGlobalAttribute(iattr)=[]; break end end for ivar=1:numel(RecordData.ListVarName) VarName=RecordData.ListVarName{ivar}; eval(['RecordData.' VarName '=squeeze(RecordData.' VarName ');']) %remove singletons end % add time dimension and update VarDimIndex: %if ~isequal(Series.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode for ivar=1:length(Field.ListVarName) % vardimindex=Field.VarDimIndex{ivar};% array of dimension indices for variable VarIndex(ivar) DimCell=Field.VarDimName(ivar); if testsum(ivar)==2%variable used as time series % RecordData.VarDimIndex{ivar}=[1 vardimindex+1]; RecordData.VarDimName{ivar}=[{'Time'} DimCell]; elseif testsum(ivar)==1 % RecordData.VarDimIndex{ivar}=[vardimindex+1]; RecordData.VarDimName{ivar}=DimCell; end end % end indexremove=find(~testsum); if ~isempty(indexremove) RecordData.ListVarName(1+indexremove)=[]; RecordData.VarDimName(indexremove)=[]; if isfield(RecordData,'Role')&~isempty(RecordData.Role{1})%generaliser aus autres attributs RecordData.Role(1+indexremove)=[]; end end %RecordData.VarDimIndex=[{[1]} RecordData.VarDimIndex]; %time dimension %shift variable attributes if isfield(RecordData,'VarAttribute') RecordData.VarAttribute=[{[]} RecordData.VarAttribute]; end RecordData.VarDimName=[{'Time'} RecordData.VarDimName]; RecordData.Action=Series.Action;%name of the processing programme %name of result file [filemean]=... name_generator(filebase_out,num_i1{1}(i_slice),num_j1{1}(i_slice),'.nc','_i1-i2_j1-j2',1,num_i2{end}(ifile),num_j2{end}(ifile),SubDir{1}); errormsg=struct2nc(filemean,RecordData); %save result file if isempty(errormsg) display([filemean ' written']) else msgbox_uvmat('ERROR',['error in Series/struct2nc' errormsg]) end end figure haxes=axes; plot_field(RecordData,haxes) hget_field=findobj(allchild(0),'name','get_field'); if ~isempty(hget_field) delete(hget_field) end get_field(filemean,RecordData) %----------------------------------------------------------------------- % --- Executes on selection change in CoordType. function CoordType_Callback(hObject, eventdata, handles) menu_str=get(handles.CoordType,'String'); ind_coord=get(handles.CoordType,'Value'); coord_option=menu_str{ind_coord}; if isequal(coord_option,'more...'); fct_name=''; if exist('./TMP/current_usr_fct.mat','file')% if a file is found h=load('./TMP/current_usr_fct.mat'); if isfield(h,'fct_name'); fct_name=h.fct_name; end end prompt = {'Enter the name of the transform function'}; dlg_title = 'user defined transform'; num_lines= 1; [FileName, PathName, filterindex] = uigetfile( ... {'*.m', ' (*.m)'; '*.m', '.m files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file', fct_name); fct_name=fullfile(PathName,FileName); addpath(PathName);%add the path to the selected fct [errormsg,date_str]=check_functions;%check whether new functions can oversed the uvmat package A UTILISER if ~exist(fct_name,'file') warndlg(['image procesing fct ' fct_name ' not found']) else transform=FileName(1:end-2);% update_menu(handles.CoordType,transform)%add the selected fct to the menu % set(handles.mouse_coord,'String',menu([1:end-1])')%update the mouse coord menu %save ('./TMP/current_usr_fct.mat','fct_name'); end end ind_coord=get(handles.CoordType,'Value'); %--------------------------------------------------------------------- % % --- Executes on selection change in ProjObject. % function ProjObject_Callback(hObject, eventdata, handles) % % list_object=get(handles.ProjObject,'String'); % index=get(handles.ProjObject,'Value'); % hseries=get(handles.ProjObject,'Parent'); % SeriesData=get(hseries,'UserData'); % Obj=SeriesData.ProjObject{index}; % [SeriesData.hset_object,SeriesData.sethandles]=set_object(SeriesData.ProjObject{index}); % set(hseries,'UserData',SeriesData);