%'merge_proj_volume': concatene several fields from series, project on volumes %------------------------------------------------------------------------ % function ParamOut=merge_proj_volume(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 2008-2022, 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=merge_proj_volume(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='on';% 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='off';% 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='off';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.volume';%set the output dir extension ParamOut.OutputFileMode='NbInput_i';% '=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 ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) 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']) end return end %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% ParamOut=[]; %default output RUNHandle=[]; WaitbarHandle=[]; %% 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; else 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 end if ~(isfield(Param,'ProjObject') && strcmp(Param.ProjObject.Type,'volume')&& strcmp(Param.ProjObject.ProjMode,'interp_lin')) msgbox_uvmat('ERROR','a projection object of type volume with ProjMode interp_lin must be introduced') return 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 %%%%%%%%%%%% 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 %% define the name for result file (with path=RootPath{1}) OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files if ~isfield(Param,'InputFields') Param.InputFields.FieldName=''; end %% determine the file type on each line from the first input file ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; 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 if CheckImage{iview} ParamIn{iview}=MovieObject{iview}; else ParamIn{iview}=Param.InputFields; end 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 %% check calibration data for iview=1:NbView if isfield(XmlData{iview}.GeometryCalib,'CheckVolumeScan') %old convention (<2022) CheckVolumeScan{iview}=XmlData{iview}.GeometryCalib.CheckVolumeScan; XmlData{iview}.Slice.SliceCoord=XmlData{iview}.GeometryCalib.SliceCoord; XmlData{iview}.Slice.SliceAngle=XmlData{iview}.GeometryCalib.SliceAngle; elseif isfield(XmlData{1},'Slice')&& isfield(XmlData{iview}.Slice,'CheckVolumeScan') %new convention (>=2022) CheckVolumeScan{iview}=XmlData{iview}.Slice.CheckVolumeScan; else disp('no volume info in calibration data (xml file)') return end if CheckVolumeScan{iview}==0 disp('input field sereis with volume scan (index j) is needed') return end end %% initiate output field DataVol.ListGlobalAttribute={'Conventions','CoordUnit','Time'}; DataVol.Conventions='uvmat'; DataVol.CoordUnit=XmlData{1}.GeometryCalib.CoordUnit; DataVol.Time=0; %TO UPDATE DataVol.ListVarName={'coord_x','coord_y','coord_z','A'}; DataVol.VarDimName={'coord_x','coord_y','coord_z',{'coord_z','coord_y','coord_x'}}; DataVol.VarAttribute{1}.Role='coord_x'; DataVol.VarAttribute{2}.Role='coord_y'; DataVol.VarAttribute{3}.Role='coord_z'; DataVol.VarAttribute{4}.Role='scalar'; DataVol.coord_x=Param.ProjObject.RangeX(1):Param.ProjObject.DX:Param.ProjObject.RangeX(2); DataVol.coord_y=Param.ProjObject.RangeY(1):Param.ProjObject.DY:Param.ProjObject.RangeY(2); DataVol.coord_z=Param.ProjObject.RangeZ(1):Param.ProjObject.DZ:Param.ProjObject.RangeZ(2); DataVol.A=zeros(numel(DataVol.coord_z),numel(DataVol.coord_y),numel(DataVol.coord_x)); %% 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) % if isfield(Param,'TransformInput') % for iview=1:NbView % XmlData{iview}.TransformInput=Param.TransformInput; % end % end % end %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% % EDIT FROM HERE % %% output file type if isempty(j1_series{1}) disp('error: no index j for z position label') return end NomTypeOut='_1'; RootFileOut=RootFile{1}; for iview=2:NbView if ~strcmp(RootFile{iview},RootFile{1}) RootFileOut='mproj'; break end end %% 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 %%%%%%%%%%%%%%%% tstart=tic; %used to record the computing time CheckOverwrite=1;%default if isfield(Param,'CheckOverwrite') CheckOverwrite=Param.CheckOverwrite; end for index_i=1:NbField_i AMerge=zeros(NbField_j,numel(DataVol.coord_y),numel(DataVol.coord_x)); for index_j=1:NbField_j index_j %% generating the name of the merged field OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,'.nc',NomTypeOut,index_i); if ~CheckOverwrite && exist(OutputFile,'file') disp(['existing output file ' OutputFile ' already exists, skip to next field']) continue% skip iteration if the mode overwrite is desactivated and the result file already exists 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_j},FileType{iview},ParamIn{iview},frame_index{iview}(index_j)); if ~isempty(errormsg) disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun) return end ListVar=Data{iview}.ListVarName; for ilist=1:numel(ListVar) Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations 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 Data{iview}.ZIndex=index_j; [X,Y]=meshgrid(DataVol.coord_x,DataVol.coord_y);%grid in physical coordinates Data{iview}=proj_plane(Data{iview},XmlData{iview},X,Y); %project on the common x,y plane end % merge the NbView fields only to merge views from several cameras) % [MergeData,errormsg]=merge_field(ProjData); % if ~isempty(errormsg) % disp_uvmat('ERROR',errormsg,checkrun); % return % end AMerge(index_j,:,:)=Data{iview}.A; %%%%%%%%%%%%%%%% END LOOP FOR VOLUME SCAN %%%%%%%%%%%%%%%% end %interpolate on the vertical grid Z=zeros(1,NbField_j); for j_index=1:numel(DataVol.coord_y) for i_index=1:numel(DataVol.coord_x) for ZIndex=1:NbField_j Z(ZIndex)=Zpos(XmlData{iview},ZIndex,X(j_index,i_index),Y(j_index,i_index)); end DataVol.A(:,j_index,i_index) = interp1(Z,AMerge(:,j_index,i_index),DataVol.coord_z); end end error=struct2nc(OutputFile,DataVol)%save result file % if index==1 % TimeData.ListGlobalAttribute={'Conventions','Project','CoordUnit','TimeUnit','ZPos','Time'}; % TimeData.Conventions='uvmat'; % TimeData.Project='2016_Circumpolar'; % TimeData.CoordUnit='cm'; % TimeData.TimeUnit='s'; % % TimeData.ZPos=ZPos; % TimeData.ListVarName={'radius','azimuth','U','V','curl','div'}; % TimeData.VarDimName={'radius','azimuth',{'radius','azimuth'},{'radius','azimuth'}... % {'radius','azimuth'},{'radius','azimuth'}}; % TimeData.VarAttribute{1}.Role=''; % TimeData.VarAttribute{2}.Role=''; % TimeData.VarAttribute{3}.Role='vector_x'; % TimeData.VarAttribute{4}.Role='vector_y'; % TimeData.VarAttribute{5}.Role='scalar'; % TimeData.VarAttribute{6}.Role='scalar'; % % end % % %% append data to the netcdf file for next iterations % % % error=struct2nc(OutputFile,TimeData);%save result file % if isempty(error) % disp(['output file ' OutputFile ' written']) % else % disp(error) % end % ellapsed_time=toc(tstart); % disp(['ellapsed time since start ' num2str(ellapsed_time/60,2) ' minutes']) end % disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration']) % %'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 global attributes of the first field % NbView=length(Data); % if NbView==1% if there is only one field, just reproduce it in MergeData % 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 concatene data % for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName % VarName=Data{1}.ListVarName{ivar}; % 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 % MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) % MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; % MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; % 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 data marked by error flag % if iview==1 % %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field % MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag % 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) +double(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 % MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data % end % end % % end % end % get the X position corresponding to X,Y for a given plane (labelled by ZIndex) function Z=Zpos(XmlData,ZIndex,X,Y)% Z positions correspoonding to X,Y positions Z=XmlData.Slice.SliceCoord(ZIndex,3)*ones(size(X)); if isfield(XmlData.Slice,'SliceAngle')&&~isequal(XmlData.Slice.SliceAngle,[0 0 0]) [norm_plane(1), norm_plane(2), norm_plane(3)] =rotate_vector(XmlData.SliceAngle(ZIndex,:)*pi/180,0,0,1); Z=Z-(norm_plane(1)*(X-XmlData.Slice.SliceCoord(ZIndex,1))+norm_plane(2)*(Y-XmlData.Slice.SliceCoord(ZIndex,2)))/norm_plane(3); end % proj_plane: poject each image on a common grid given by coord_x and coord_y function DataOut=proj_plane(DataIn,XmlData,X,Y) DataOut=DataIn; %default output %% initial image coordinates [npy,npx]=size(DataIn.A); xima=0.5:npx-0.5;%image coordinates of corners yima=npy-0.5:-1:0.5; [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates %% projected coordinates Z=Zpos(XmlData,DataIn.ZIndex,X,Y);% Z positions correspoonding to X,Y positions %% interpolation on the new grid [XIMA,YIMA]=px_XYZ(XmlData.GeometryCalib,XmlData.Slice,X,Y,Z);% image coordinates for each point in the real DataOut.A=interp2(XIMA_init,YIMA_init,DataIn.A,XIMA,YIMA); %'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 global attributes of the first field NbView=length(Data); if NbView==1% if there is only one field, just reproduce it in MergeData 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 concatene data for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName VarName=Data{1}.ListVarName{ivar}; 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 MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; 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 data marked by error flag if iview==1 %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag 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) +double(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 MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data end end end end