%'aver_stat': calculate field average over a time series %------------------------------------------------------------------------ % function ParamOut=aver_stat(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 % .OutputDirExt: directory extension for data outputs % .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=aver_stat(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='.stat';%set the output dir extension return end %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% %% 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 ParamOut=Param; %default output OutputDir=[Param.OutputSubDir Param.OutputDirExt]; %% 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); [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); %%%%%%%%%%%% % 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 %%%%%%%%%%%% 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 [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 %%%%%%%%%%%% 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 %% 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 %% MAIN LOOP ON SLICES for i_slice=1:NbSlice index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice nbfiles=0; nbmissing=0; %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% for index=index_slice if checkrun stopstate=get(Param.RUNHandle,'BusyAction'); update_waitbar(Param.WaitbarHandle,index/nbfield) else stopstate='queue'; end if isequal(stopstate,'queue')% enable STOP command %%%%%%%%%%%%%%%% 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=['error of input reading: ' errormsg]; break end if ~isempty(NbSlice_calib) Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform end end else errormsg='stop'; end %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%% %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% % EDIT FROM HERE if isempty(errormsg) 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 %% calculate tps coefficients if needed if isfield(Param,'ProjObject')&&isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps') Field=tps_coeff_field(Field,check_proj_tps); end %field projection on an object if Param.CheckObject [Field,errormsg]=proj_field(Field,Param.ProjObject); if ~isempty(errormsg) msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg]) return end end nbfiles=nbfiles+1; %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% %update sum if nbfiles==1 %first field time_1=[]; if isfield(Field,'Time') time_1=Field.Time(1); end DataOut=Field;%default for ivar=1:length(Field.ListVarName) VarName=Field.ListVarName{ivar}; DataOut.(VarName)=double(DataOut.(VarName)); end else %current field for ivar=1:length(Field.ListVarName) VarName=Field.ListVarName{ivar}; sizmean=size(DataOut.(VarName)); siz=size(Field.(VarName)); if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean) msgbox_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid']) return else DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum end end end %%%%%%%%%%%% END MAIN RUNNING OPERATIONS %%%%%%%%%%%% else display(errormsg) end end %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% for ivar=1:length(Field.ListVarName) VarName=Field.ListVarName{ivar}; DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean end if nbmissing~=0 msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted']) end if isempty(time) % time is read from files if isfield(Field,'Time') time_end=Field.Time(1);%last time read if ~isempty(time_1) DataOut.Time=time_1; DataOut.Time_end=time_end; end end else % time from ImaDoc prevails if it exists % j1=1;%default % if ~isempty(j1_series{1}) % j1=j1_series{1}; % end %DataOut.Time=time(1,i1_series{1}(1),j1); %DataOut.Time_end=time(end,i1_series{end}(end),j1_series{end}(end)); DataOut.Time=time(1); DataOut.Time_end=time(end); end %writting the result file OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),i_slice,[]); if CheckImage{1} %case of images if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16)) DataOut.A=uint16(DataOut.A); imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images else DataOut.A=uint8(DataOut.A); imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images end display([OutputFile ' written']); else %case of netcdf input file , determine global attributes errormsg=struct2nc(OutputFile,DataOut); %save result file if isempty(errormsg) display([OutputFile ' written']); else msgbox_uvmat('ERROR',['error in writting result file: ' errormsg]) display(errormsg) end end % end averaging loop end %%%%%%%%%%%%%%%% end loop on slices %%%%%%%%%%%%%%%% %% open the result file with uvmat (in RUN mode) if checkrun % hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI % delete(hget_field) uvmat(OutputFile)% open the last result file with uvmat end