%'merge_proj': project and concatene fieldsmerge_proj % can be used as a template for applying an operation (here projection and concateantion) on each field of an input series %------------------------------------------------------------------------ % function GUI_config=merge_proj(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 GUI_input=merge_proj(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 GUI_input={'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) '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';'on';...%can use mask option (option 'off'/'on', 'off' by default) 'OutputDirExt';'.proj';...%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) if strcmp(Param,'input?') checkrun=1;% will inly search input parameters (preparation of BATCH mode) else Param=xml2struct(Param); checkrun=0; end % 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 checkrun=2; % indicate the RUN option is used end %% 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') 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'};%allowed input file types(images) [FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images if ~isempty(j1_series{1}) frame_index{1}=j1_series{1}; else frame_index{1}=i1_series{1}; end %% calibration data and timing: read the ImaDoc files mode=''; %default timecell={}; 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 two 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 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) || 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 %% Initiate output fields %initiate the output structure as a copy of the first input one (reproduce fields) [DataOut,ParamOut,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 %% MAIN LOOP ON SLICES %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% for i_slice=1:NbSlice index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice nbfiles=0; nbmissing=0; %initiate result fields for ivar=1:length(DataOut.ListVarName) DataOut.(DataOut.ListVarName{ivar})=0; % initialise all fields to zero end %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% for index=index_slice if checkrun update_waitbar(hseries.waitbar_frame,WaitbarPos,index/(nbfield)) stopstate=get(hseries.RUN,'BusyAction'); else stopstate='queue'; end %OUTPUT % GUI_input=list of options in the GUI series.fig needed for the function % %INPUT: % Param: structure containing all the parameters read on the GUI series % or name of the xml file containing these parameters (BATCH case) % %% projection object test_object=get(hseries.GetObject,'Value'); if test_object hset_object=findobj(allchild(0),'tag','set_object'); %ProjObject=read_set_object(guidata(hset_object)); ProjObject=read_GUI(hset_object); if ~isfield(ProjObject,'Type') msgbox_uvmat('ERROR','Undefined projection object type') return end if ~isequal(ProjObject.Type,'plane')|| isequal(ProjObject.ProjMode,'projection') msgbox_uvmat('ERROR','The projection object must be a plane with projection mode interp or filter') return end answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Type]); if ~isequal(answeryes,'Yes') return end end %% features of the input fields RootPath=Param.InputTable(:,1); RootFile=Param.InputTable(:,3); SubDir=Param.InputTable(:,2); NomType=Param.InputTable(:,4); FileExt=Param.InputTable(:,5); nbview=length(RootFile);%number of views (file series to merge) nbfield=size(i1_series{1},1)*size(i1_series{1},2);%number of fields in the time series hhh=which('mmreader'); for iview=1:nbview test_movie(iview)=0; if ~isempty(hhh) if isequal(lower(FileExt{iview}),'.avi') MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); test_movie(iview)=1; end end end %% Calibration data and timing: read the ImaDoc files timecell={}; itime=0; NbSlice_calib={}; %test for z index 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); if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) msgbox_uvmat('WARNING','inconsistent number of Z indices for the two 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 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 more than ' num2str(diff_time)]) end time=sqeeze(mean(time,1)); end % if size(time,2) < i2_series{1}(end) || size(time,3) < j2_series{1}(end)% ime array absent or too short in ImaDoc xml file' % time=[]; % end %% Field and velocity type (the same for all views) FieldName=''; if isfield(Param,'InputFields')&&isfield(Param.InputFields,'FieldMenu') FieldName=Param.InputFields.FieldMenu;%the same set of fields for all views VelType=Param.InputFields.VelTypeMenu; end % if strcmp(get(hseries.FieldMenu,'Visible'),'on') % Field_str=get(hseries.FieldMenu,'String'); % val=get(hseries.FieldMenu,'Value'); % FieldName=Field_str(val);%the same set of fields for all views % VelType_str=get(hseries.VelTypeMenu,'String'); % VelType_val=get(hseries.VelTypeMenu,'Value'); % VelType=VelType_str{VelType_val}; %the same for all views if strcmp(FieldName,'') msgbox_uvmat('ERROR','no input field defined in FieldMenu') elseif strcmp(FieldName,'get_field...') hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI end % end %detect whether all the files are 'images' or 'netcdf' testima=0; testvol=0; testcivx=0; testnc=0; 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('ERROR','need a set of images or a set of netcdf files with the same fields as input') return end if ~isequal(FieldName,'get_field...') testcivx=testnc; end %% name of output files and directory: ProjectDir=fileparts(fileparts(RootPath{1}));% preoject directory (GERK) prompt={['result directory (in' ProjectDir ')']}; % RootPath=get(hseries.RootPath,'String'); % SubDir=get(hseries.SubDir,'String'); if isequal(length(RootPath),1) fulldir=RootPath{1}; subdir='merge_proj'; res_subdir=fullfile(fulldir,subdir); else def={fullfile(ProjectDir,'0_RESULTS')}; dlgTitle='result directory'; lineNo=1; answer=msgbox_uvmat('INPUT_TXT',dlgTitle,def); fulldir=answer{1}; subdir=[]; dirlist=sort(RootFile); for iview=1:nbview if ~isempty(subdir) subdir=[subdir '-']; end subdir=[subdir dirlist{iview}]; end res_subdir=fullfile(fulldir,subdir); end ext=FileExt{1}; if ~exist(fulldir,'dir') msgbox_uvmat('ERROR',['directory ' fulldir ' needs to be created']) return end if ~exist(res_subdir,'dir') dircur=pwd; cd(fulldir); succeed=mkdir(subdir); if succeed [xx,msg2] = fileattrib(res_subdir,'+w','g'); %yield writing access (+w) to user group (g) if ~strcmp(msg2,'') msgbox_uvmat('ERROR',['pb of permission for ' res_subdir ': ' msg2])%error message for directory creation cd(dircur) return end cd(dircur); else msgbox_uvmat('ERROR',['Cannot create directory ' fulldir]) return end end filebasesub=fullfile(res_subdir,RootFile{1}); %filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files %% MAIN LOOP for ifile=1:nbfield stopstate=get(hseries.RUN,'BusyAction'); if isequal(stopstate,'queue')% enable STOP command from the 'series' interface update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) %% ----------LOOP ON VIEWS---------------------- nbtime=0; for iview=1:nbview %name of the current file 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') msgbox_uvmat('ERROR',['missing input file' filename]) break end timeread(iview)=0; %reading the current file if testima if test_movie(iview) Field{iview}.A=read(MovieObject{iview},i1_series{iview}(ifile)); else Field{iview}.A=imread(filename); end % TODO: introduce ListVarName npxy=size(Field{iview}.A); Field{iview}.ListVarName={'AX','AY','A'}; Field{iview}.VarDimName={'AX','AY',{'AY','AX'}}; Field{iview}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers Field{iview}.AY=[npxy(1)-0.5 0.5]; Field{iview}.CoordUnit='pixel'; Field{iview}.AName='image'; else if testcivx [Field{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); else [Field{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data Field{iview}.VarAttribute=SubField.VarAttribute; end if isfield(Field{iview},'Txt') msgbox_uvmat('ERROR',Field{iview}.Txt) return end if isfield(Field{iview},'Time') timeread(iview)=Field{iview}.Time; nbtime=nbtime+1; end end if ~isempty(NbSlice_calib) Field{iview}.ZIndex=mod(i1_series{iview}(ifile)-1,NbSlice_calib{1})+1; end %transform the input field (e.g; phys) if requested if ~isempty(transform_fct) Field{iview}=transform_fct(Field{iview},XmlData{iview}); %transform to phys if requested end if testcivx Field{iview}=calc_field(FieldName,Field{iview}); end %projection on object (gridded plane) if test_object [Field{iview},errormsg]=proj_field(Field{iview},ProjObject); if ~isempty(errormsg) msgbox_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg]) return end end end %----------END LOOP ON VIEWS---------------------- %% merge the nbview fields MergeData=merge_field(Field); if isfield(MergeData,'Txt') msgbox_uvmat('ERROR',MergeData.Txt) return end % generating the name of the merged field if testima ResultExt='.png'; else ResultExt=FileExt{iview}; end i1=i1_series{iview}(ifile); if ~isempty(i2_series{iview}) i2=i2_series{iview}(ifile); else i2=i1; end j1=1; j2=1; if ~isempty(j1_series{iview}) j1=j1_series{iview}(ifile); if ~isempty(j2_series{iview}) j2=j2_series{iview}(ifile); else j2=j1; end end mergename=fullfile_uvmat(res_subdir,'','merged',ResultExt,NomType{iview},i1,i2,j1,j2); % mergename=name_generator(filebase_merge,i1,j1_series{iview}(ifile),ResultExt,NomType{iview},1,i2_series{iview}(ifile),j2_series{iview}(ifile)); % time of the merged field: time_i=0;%default if isempty(time)% time from ImaDoc prevails time_i=sum(timeread)/nbtime; else % time_i=i1; time_i=(time(i1,j1)+time(i2,j2))/2; %TODO: upgrade end % recording the merged field if testima %in case of input images an image is produced if isa(MergeData.A,'uint8') bitdepth=8; elseif isa(MergeData.A,'uint16') bitdepth=16; end imwrite(MergeData.A,mergename,'BitDepth',bitdepth); %write xml calibration file siz=size(MergeData.A); npy=siz(1); npx=siz(2); if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') Rangx=MergeData.VarAttribute{1}.Coord_2; Rangy=MergeData.VarAttribute{1}.Coord_1; elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') Rangx=[MergeData.AX(1) MergeData.AX(end)]; Rangy=[MergeData.AY(1) MergeData.AY(end)]; else Rangx=[0.5 npx-0.5]; Rangy=[npy-0.5 0.5];%default end pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); T_x=-pxcmx*Rangx(1)+0.5; T_y=-pxcmy*Rangy(2)+0.5; GeometryCal.focal=1; GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; ImaDoc.GeometryCalib=GeometryCal; t=struct2xml(ImaDoc); t=set(t,1,'name','ImaDoc'); save(t,[filebase_merge '.xml']) display([filebase_merge '.xml saved']) else MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; MergeData.Conventions='uvmat'; MergeData.nb_coord=2; MergeData.nb_dim=2; dt=[]; if isfield(Field{1},'dt')&& isnumeric(Field{1}.dt) dt=Field{1}.dt; end for iview =2:numel(Field) if ~(isfield(Field{iview},'dt')&& isequal(Field{iview}.dt,dt)) dt=[];%dt not the same for all fields end end if isempty(dt) MergeData.ListGlobalAttribute(6)=[]; else MergeData.dt=dt; end MergeData.Time=time_i; error=struct2nc(mergename,MergeData);%save result file if isempty(error) display(['output file ' mergename ' written']) else display(error) end end end end %'merge_field': concatene fields %------------------------------------------------------------------------ function MergeData=merge_field(Data) %% default output if isempty(Data)||~iscell(Data) MergeData=[]; return end MergeData=Data{1};%default error=0; nbview=length(Data); if nbview==1 return end %% group the variables (fields of 'FieldData') in cells of variables with the same dimensions [CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1}); %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS % CellVarIndex=cells of variable index arrays ivar_new=0; % index of the current variable in the projected field for icell=1:length(CellVarIndex) if NbDim(icell)==1 continue end VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName VarType=VarTypeCell{icell}; ivar_X=VarType.coord_x; ivar_Y=VarType.coord_y; ivar_FF=VarType.errorflag; if isempty(ivar_X) test_grid=1;%test for input data on regular grid (e.g. image)coordinates else if length(ivar_Y)~=1 msgbox_uvmat('ERROR','y coordinate missing in proj_field.m') return end test_grid=0; end %case of input fields with unstructured coordinates if ~test_grid for ivar=VarIndex VarName=MergeData.ListVarName{ivar}; for iview=1:nbview eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName '];']) end end %case of fields defined on a structured grid else testFF=0; for iview=2:nbview for ivar=VarIndex VarName=MergeData.ListVarName{ivar}; if isfield(MergeData,'VarAttribute') if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') testFF=1; end end eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';']) end end if testFF nbaver=nbview-MergeData.FF; indgood=find(nbaver>0); for ivar=VarIndex VarName=MergeData.ListVarName{ivar}; eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);']) end else for ivar=VarIndex VarName=MergeData.ListVarName{ivar}; eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;']) end end end end