%'merge_proj': concatene several fields from series, can project them on a regular grid in phys coordinates %------------------------------------------------------------------------ % function ParamOut=merge_proj(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 2008-2014, LEGI UMR 5519 / CNRS UJF 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=merge_proj(Param) %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed 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='off'; %nbre of slices ('off' by default) ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) ParamOut.FieldName='one';% 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.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) ParamOut.ProjObject='on';%can use projection object(option 'off'/'on', ParamOut.Mask='on';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.mproj';%set the output dir extension ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice %check the input files first_j=[]; if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_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']) elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject') msgbox_uvmat('WARNING','You may need a projection object of type plane for merge_proj') end return end %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% 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];% subdirectory for output files if ~isfield(Param,'InputFields') Param.InputFields.FieldName=''; end %% root input file 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 %% 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') 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}=~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 if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject') disp_uvmat('ERROR','projection on a common grid is needed to concatene images: use a Projection Object of type ''plane'' with ProjMode=''interp_lin''',checkrun) return 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) ': the mean time is chosen in result'],checkrun) end end if ~isempty(errormsg) disp_uvmat('WARNING',errormsg,checkrun) end time=mean(time,1); %averaged time taken for the merged field %% coordinate transform or other user defined transform transform_fct='';%default fct handle if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) currentdir=pwd; cd(Param.FieldTransform.TransformPath) transform_fct=str2func(Param.FieldTransform.TransformName); cd (currentdir) end %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% % EDIT FROM HERE %% check the validity of input file types for iview=1:NbView if ~isequal(CheckImage{iview},1)&&~isequal(CheckNc{iview},1) disp_uvmat('ERROR','input set of input series: need either netcdf either image series',checkrun) return end end %% output file type if min(cell2mat(CheckImage))==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane')) FileExtOut='.png'; %image output (input and proj result = image) for iview=1:NbView BitDepth(iview)=FileInfo{iview}.BitDepth; end BitDepth=max(BitDepth); else FileExtOut='.nc'; %netcdf output end NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series RootFileOut=RootFile{1}; for iview=2:NbView if ~strcmp(RootFile{iview},RootFile{1}) RootFileOut='mproj'; break end end %% mask (TODO: case of multilevels) MaskData=cell(NbView,1); if Param.CheckMask if ischar(Param.MaskTable)% case of a single mask (char chain) Param.MaskTable={Param.MaskTable}; end for iview=1:numel(Param.MaskTable) if exist(Param.MaskTable{iview},'file') [MaskData{iview},tild,errormsg] = read_field(Param.MaskTable{iview},'image'); if ~isempty(transform_fct) && nargin(transform_fct)>=2 MaskData{iview}=transform_fct(MaskData{iview},XmlData{iview}); end end end end %% Set field names and velocity types %use Param.InputFields for all views %% MAIN LOOP ON FIELDS %%%%%%%%%%%%% 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; %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% for index=1:NbField update_waitbar(WaitbarHandle,index/NbField) if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') return end %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% Data=cell(1,NbView);%initiate the set Data timeread=zeros(1,NbView); for iview=1:NbView %% reading input file(s) [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index)); if ~isempty(errormsg) disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun) return end % get the time defined in the current file if not already defined from the xml file if ~isempty(time) && isfield(Data{iview},'Time') timeread(iview)=Data{iview}.Time; end if ~isempty(NbSlice_calib) Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform end %% transform the input field (e.g; phys) if requested (no transform involving two input fields) if ~isempty(transform_fct) if nargin(transform_fct)>=2 Data{iview}=transform_fct(Data{iview},XmlData{iview}); else Data{iview}=transform_fct(Data{iview}); end end %% calculate tps coefficients if needed check_proj_tps= isfield(Param,'ProjObject')&&~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'interp_tps')&&~isfield(Data{iview},'Coord_tps'); Data{iview}=tps_coeff_field(Data{iview},check_proj_tps); %% projection on object (gridded plane) if Param.CheckObject [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject); if ~isempty(errormsg) disp_uvmat('ERROR',['ERROR in merge_proge/proj_field: ' errormsg],checkrun) return end end %% mask if Param.CheckMask && ~isempty(MaskData{iview}) [Data{iview},errormsg]=mask_proj(Data{iview},MaskData{iview}); end end %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%% %% merge the NbView fields [MergeData,errormsg]=merge_field(Data); if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun); return end %% time of the merged field: take the average of the different views if ~isempty(time) timeread=time(index); elseif ~isempty(find(timeread))% time defined from ImaDoc timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined) else timeread=index;% take time=file index end %% generating the name of the merged field i1=i1_series{1}(index); if ~isempty(i2_series{end}) i2=i2_series{end}(index); else i2=i1; end j1=1; j2=1; if ~isempty(j1_series{1}) j1=j1_series{1}(index); if ~isempty(j2_series{end}) j2=j2_series{end}(index); else j2=j1; end end OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,FileExtOut,NomType{1},i1,i2,j1,j2); %% recording the merged field if strcmp(FileExtOut,'.png') %output as image if BitDepth==8 imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8) else imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16) end if index==1 %write xml calibration file, using the first file siz=size(MergeData.A); npy=siz(1); npx=siz(2); if isfield(MergeData,'coord_x') && isfield(MergeData,'coord_y') Rangx=MergeData.coord_x; Rangy=MergeData.coord_y; 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.CalibrationType='rescale'; GeometryCal.CoordUnit=MergeData.CoordUnit; 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,[fileparts(OutputFile) '.xml']) end else MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim'}; MergeData.Conventions='uvmat'; MergeData.nb_coord=2; MergeData.nb_dim=2; dt=[]; if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt) dt=Data{1}.dt; end for iview =2:numel(Data) if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt)) dt=[];%dt not the same for all fields end end if ~isempty(timeread) MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'Time'}]; MergeData.Time=timeread; end if ~isempty(dt) MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'dt'}]; MergeData.dt=dt; end error=struct2nc(OutputFile,MergeData);%save result file if isempty(error) disp(['output file ' OutputFile ' written']) else disp(error) end end end %'merge_field': concatene fields %------------------------------------------------------------------------ function [MergeData,errormsg]=merge_field(Data) %% default output if isempty(Data)||~iscell(Data) MergeData=[]; return end errormsg=''; MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field NbView=length(Data); if NbView==1 return end %% group the variables (fields of 'Data') in cells of variables with the same dimensions [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); if ~isempty(errormsg) return end %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS for icell=1:length(CellInfo) if NbDim(icell)~=1 % skip field cells which are of dim 1 switch CellInfo{icell}.CoordType case 'scattered' %case of input fields with unstructured coordinates: just concacene data for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName VarName=Data{1}.ListVarName{ivar}; %MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field for iview=2:NbView MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; end end case 'grid' %case of fields defined on a structured grid FFName=''; if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable end % select good data on each view for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName VarName=Data{1}.ListVarName{ivar}; for iview=1:NbView if isempty(FFName) check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else else check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else end Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or masked data if iview==1 MergeData.(VarName)=Data{1}.(VarName);% correct the field of MergeData NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; return else MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName);%add data NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else end end MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point end end if isempty(FFName) FFName='FF'; end MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data end end