%'aver_stat': calculate field average over a time series %------------------------------------------------------------------------ % function ParamOut=aver_stat(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=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)% 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 = '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 ParamOut.OutputFileMode='NbSlice';% '=NbInput': one output file per input file index, '=NbInput_i': one file per input file index i, '=NbSlice': one file per slice % check for selection of a projection object hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series if ~isfield(Param,'ProjObject') answer=msgbox_uvmat('INPUT_Y-N','use a projection object?'); if strcmp(answer,'Yes') hhseries=guidata(hseries); set(hhseries.CheckObject,'Visible','on') set(hhseries.CheckObject,'Value',1) Param.CheckObject=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 % 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 % determine volume scan mode prompt = {'volume scan mode (Yes/No)'}; dlg_title = 'determine volume scan'; num_lines= 1; def = { 'No'}; answer=msgbox_uvmat('INPUT_Y-N','volume scan mode (OK/No)?'); % answer = inputdlg(prompt,dlg_title,num_lines,def); if isempty(answer) return end %check input consistency if strcmp(answer,'Yes') ParamOut.NbSlice=1;% set NbSlice to 1 ( for i index) ParamOut.ActionInput.CheckVolume=1; 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 NcTypeOptions={'netcdf','civx','civdata'}; 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; CheckImage{iview}=strcmp(FileInfo{iview}.FieldType,'image');% =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 disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) 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) if isfield(Param,'TransformInput') XmlData{1}.TransformInput=Param.TransformInput; end end %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% % EDIT FROM HERE %% check the validity of input file types and set the output file type 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 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 if isfield(Param,'ProjObject') && ~strcmp(Param.ProjObject.Type,'plane') FileExtOut='.nc';% write result as .nc files (even for image input) end %% settings for the output file 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 VarMesh=[]; if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}) 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 aver_stat again to set the value',checkrun) end end NbSlice_j=1;% number of j slices =1 except fo volume scan index_series=1:size(filecell,2); index_j=1; %% set volume scan if requested first_j_out=first_j;%first j index to use for the output file name last_j_out=last_j;%last j index to use for the output file name if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'CheckVolume') ... && Param.ActionInput.CheckVolume index_j=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j; NbSlice_j=numel(index_j); index_series=1:NbSlice_j:size(filecell,2); end %% loop on j slices (volume scan) for islice=index_j nbfiles=0;%counter of the successfully read files (bad files are skipped) if NbSlice_j>1 first_j_out=islice;%first and last j index to use for the output file name are the current j index last_j_out=islice; end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% for index=index_series+index_j(islice)-index_j(1) update_waitbar(WaitbarHandle,index/NbField) if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') break end %%%%%%%%%%%%%%%% 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% leave the loop on views in case of error end if ~isempty(NbSlice_calib) Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform end end %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%% if ~isempty(errormsg) disp(errormsg) continue % go to next input field in case of error (file skipped in the average) end Field=Data{1}; % default input field structure nbfiles=nbfiles+1; %increment the file counter %% 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 if strcmp(Param.ProjObject.ProjMode,'interp_tps') Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed end [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh); if ~isempty(errormsg) disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun) return end end %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% if nbfiles==1 %first field time_1=[]; if isfield(Field,'Time') time_1=Field.Time(1); end DataOut=Field;%outcome reproduces the first (projected) field by default DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram) VarName=Field.ListVarName{ivar}; if isfield(Data{1},VarName) DataOut.(VarName)=Field.(VarName); DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName))); VarMesh=DataOut.(VarName)(2)-DataOut.(VarName)(1); end end disp(['mesh for histogram = ' num2str(VarMesh)]) else errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable if isfield(Field,'VarAttribute') for ivar=1:numel(Field.ListVarName) VarName=Field.ListVarName{ivar}; DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero for iivar=1:length(Field.VarAttribute) if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')... && strcmp(Field.VarAttribute{iivar}.Role,'errorflag') errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar end end end DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result else for ivar=1:numel(Field.ListVarName) VarName=Field.ListVarName{ivar}; DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero end end end end %current field for ivar=1:length(DataOut.ListVarName) VarName=DataOut.ListVarName{ivar}; sizmean=size(DataOut.(VarName)); siz=size(Field.(VarName)); if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}) if isfield(Data{1},VarName) MaxValue=max(DataOut.(VarName));% current max of histogram absissa MinValue=min(DataOut.(VarName));% current min of histogram absissa % VarMesh=Field.VarAttribute{ivar}.Mesh; 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(1,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(1,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'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)=... DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']); end elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean) disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid'],checkrun) return else if errorvar(ivar)==0 check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else else check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else end Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point end end %%%%%%%%%%%% END MAIN RUNNING OPERATIONS %%%%%%%%%%%% end %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})) for ivar=1:length(Field.ListVarName) VarName=Field.ListVarName{ivar}; DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean end end nbmissing=numel(index_series+index_j(islice)-index_j(1))-nbfiles; if nbmissing~=0 if NbSlice_j==1 disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun) else disp(['WARNING: ' num2str(nbmissing) ' input files are missing or skipped in slice ' num2str(islice)]) end 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 DataOut.Time=time(1); DataOut.Time_end=time(end); end %% writing the result file OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out); if strcmp(FileExtOut,'.png') %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 disp([OutputFile ' written']); else %case of netcdf file , determine global attributes errormsg=struct2nc(OutputFile,DataOut); %save result file if isempty(errormsg) disp([OutputFile ' written']); else disp(['error in writting result file: ' errormsg]) end end % end averaging loop end %% open the result file with uvmat (in RUN mode) if checkrun uvmat(OutputFile)% open the last result file with uvmat end