%---------------------------------------------------------------------- % -process LIF images %---------------------------------------------------------------------- function GUI_input=LIF_series(num_i1,num_i2,num_j1,num_j2,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';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) 'FieldMenu';'one';...% 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 of the GUI series WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame %------------------------------------------------- addpath '/fsnet/project/coriolis/2006/06ICEBOX/0_MATLAB_WORK/LIF'% define path for concentration.m % cpath=which('series'); %mode=''; %default time=[]; nbviews=numel(Series.RootPath); if nbviews<2 msgbox_uvmat('ERROR','enter both LIF and PIV series')% we introduce PIV series to improve the filtering (remove particle image) return end [PD,LIFdir]=fileparts(Series.RootPath{1}); fulldir=fullfile(PD,'Concentration'); if ~exist(fulldir,'dir') try mkdir(fulldir) [xx,msg2] = fileattrib(fulldir,'+w','g'); %yield writing access (+w) to user group (g) catch ME msgbox_uvmat('ERROR',ME.message) return end end filebase_LIF=fullfile(fulldir,'LIF');%root name for the merged files RootPath=Series.RootPath{1}; filebase=fullfile(Series.RootPath{1},Series.RootFile{1});%root file name filebase_1=fullfile(Series.RootPath{2},Series.RootFile{2});%root file name for PIV (background correction) nbfield=numel(num_i1{1});%number of fields in the series [XmlData,error]=imadoc2struct([filebase '.xml']);% calibration data for LIF %[error,Heading,nom_type_read,ext_ima_read,tt,TimeUnit,mode,NbSlice,npx,npy,Calib{2}] [XmlData_1,error]=imadoc2struct([filebase_1 '.xml']);% calibration data for PIV if isfield(XmlData,'Time') time=XmlData.Time; if isfield(XmlData_1,'Time') time_1=XmlData_1.Time; if ~isequal(size(time),size(time_1)) msgbox_uvmat('WARNING','inconsistent time array lengths in ImaDoc fields') end end end %check coincidence in time if size(time,1)>1 diff_time=max(max(abs(time-time_1))) if diff_time>0 msgbox_uvmat(['times of series differ by more than ' num2str(diff_time)],'WARNING') end end hRUN=findobj(Series.hseries,'Tag','RUN');%handles the the uicontrol 'RUN' itime=0; %%%%%% %LOOP ON FILES RootPath=fullfile(RootPath,'LIF_REF'); for ifile=1:nbfield stopstate=get(hRUN,'BusyAction');%enable stop button if isequal(stopstate,'queue')% enable STOP command update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) %name of the current LIF input file [inputfile,idetect]=name_generator(filebase,num_i1{1}(ifile),num_j1{1}(ifile),Series.FileExt{1},Series.NomType{1},1,num_i1{1}(ifile),num_j2{1}(ifile)); if ~idetect msgbox_uvmat('ERROR',[inputfile ' not found']) return end [Data,ParamOut,errormsg] = read_field(inputfile,'image',[]); Data.ZIndex=num_i1{1}(ifile)-Series.NbSlice*(floor((num_i1{1}(ifile)-1)/Series.NbSlice));%second field index file_ref=fullfile(RootPath,['lif_ref_' num2str(Data.ZIndex) '.nc']); Ref=nc2struct(file_ref);%reference file [inputfile_1,idetect]=name_generator(filebase_1,num_i1{2}(ifile),num_j1{2}(ifile),Series.FileExt{2},Series.NomType{2},1,num_i2{2}(ifile),num_j2{2}(ifile)); if ~idetect msgbox_uvmat('ERROR',[inputfile_1 ' not found']) return end Data_1=read_field(inputfile_1,'image',{[]});% read the image Data_1.ZIndex=Data.ZIndex; %%% transform image to concentration [DataOut,dd,DataMask]=concentration(Data,XmlData,Data_1,XmlData_1,Ref); % output file name (netcdf) outputfile=name_generator(filebase_LIF,num_i1{1}(ifile),num_j1{1}(ifile),'.nc',Series.NomType{2},1,num_i2{1}(ifile),num_j2{1}(ifile)); % create a structure to prepare the result file Resu.ListGlobalAttribute={'Project','InputFile_1','InputFile_2','Action','Time','ZIndex','z'}; [PP,Resu.Project]=fileparts(Series.PathProject); Resu.InputFile_1=inputfile; Resu.InputFile_2=inputfile_1; Resu.Action=Series.Action; if isempty(time) Resu.Time=0; else Resu.Time=time(num_i1{1}(ifile),num_j1{1}(ifile)); end Resu.ZIndex=Data.ZIndex; Resu.z=XmlData.GeometryCalib.SliceCoord(Data.ZIndex,3); Resu.ListVarName={'AY' ,'AX' ,'c','mask'}; Resu.VarDimName={'AY','AX',{'AY','AX'},{'AY','AX'}}; Resu.AY=[DataOut.AY(1), DataOut.AY(end)]; Resu.AX=[DataOut.AX(1), DataOut.AX(end)]; Resu.c=DataOut.A; Resu.mask=DataMask.A;%to chnge to cartesian coordinates (polar2phys) error=struct2nc(outputfile,Resu); %save result file if isempty(error) display(['output file ' outputfile ' written']) else display( error) end end end