function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series); %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) if ~exist('num_i1','var') GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) 'RootFile';'on';... %root input file name ('on' by default) 'FileExt';'on';... %input file extension ('on' by default) 'NomType';'on';...%type of file indexing ('on' by default) 'NbSlice';'on'; ...%nbre of slices ('off' by default) 'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) 'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) 'CoordType';'on';...%can use a transform function 'off' by default 'GetObject';'on';...%can use projection object ,'off' by default %'GetMask';'on'...%can use mask option ,'off' by default %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter ''}; return %exit the function end %------------------------------------------------- hseries=guidata(Series.hseries);%handles of the GUI series WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame %------------------------------------------------- %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)); if ~isfield(ProjObject,'Style') msgbox_uvmat('ERROR','Undefined projection object style') return end if ~isequal(ProjObject.Style,'plane') msgbox_uvmat('ERROR','The projection object must be a plane') return end %answeryes=questdlg({['field series projected on ' Series.ProjObject.Style]}); answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Style]); if ~isequal(answeryes,'Yes') return end end %numbers of view fields (nbre of inputs in RootPath) testcell=iscell(Series.RootFile); if ~testcell Series.RootPath={Series.RootPath}; Series.RootFile={Series.RootFile}; Series.SubDir={Series.SubDir}; Series.FileExt={Series.FileExt}; Series.NomType={Series.NomType}; num_i1={num_i1}; num_i2={num_i2}; num_j1={num_j1}; num_j2={num_j2}; end nbview=length(Series.RootFile);%number of views (file series to merge) nbfield=size(num_i1{1},1)*size(num_i1{1},2);%number of fields in the time series transform=Series.CoordType; % field transform function hhh=which('mmreader'); for iview=1:nbview test_movie(iview)=0; if ~isequal(hhh,'')&& mmreader.isPlatformSupported() 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 mode=''; %default timecell={}; itime=0; NbSlice_calib={}; %test for z index for iview=1:nbview%Loop on views XmlData{iview}=[];%default filebase{iview}=fullfile(Series.RootPath{iview},Series.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 length(timecell)==0 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 end if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' time=[]; end % coordinate transform or other user defined transform transform_fct=[];%default if isfield(Series,'transform_fct') transform_fct=Series.transform_fct; end % Field and velocity type (the same for all views) 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 isequal(FieldName,'get_field...') hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI % hhget_field=guidata(hget_field);%handles of GUI elements in get_field SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI % if isequal(get(hhget_field.menu_coord,'Visible'),'on') % list_transform=get(hhget_field.menu_coord,'String'); % val_list=get(hhget_field.menu_coord,'Value'); % transform=list_transform{val_list}; % end end %detect whether all the files are 'images' or 'netcdf' testima=0; testvol=0; testcivx=0; testnc=0; FileExt=get(hseries.FileExt,'String'); 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: % res_subdir=fullfile(Series.RootPath{1},[Series.SubDir{1} '_STAT']); ProjectDir=fileparts(fileparts(Series.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(Series.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) error=mkdir(subdir); cd(dircur) end filebasesub=fullfile(res_subdir,Series.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) Amerge=0; %----------LOOP ON VIEWS---------------------- nbtime=0; for iview=1:nbview %name of the current file filename=name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview}); if ~exist(filename,'file') msgbox_uvmat('ERROR',['missing input file' filename]) break end %reading the current file if testima if test_movie(iview) Field{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile)); else Field{iview}.A=imread(filename); end % TODO: introduce ListVarName npxy=size(Field{iview}.A); 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}.CoordType='px'; 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},'Time') timeread(iview)=Field{iview}.Time; nbtime=nbtime+1; end end % coord transform % z index if ~isempty(NbSlice_calib) Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1; end 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}=proj_field(Field{iview},ProjObject); 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 mergename=name_generator(filebase_merge,num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile)); % time: time_i=0;%default if isempty(time)% time from ImaDoc prevails time_i=sum(timeread)/nbtime; else time_i=(time(iview,num_i1{iview}(ifile),num_j1{iview}(ifile))+time(iview,num_i2{iview}(ifile),num_j2{iview}(ifile)))/2; 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={'Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; MergeData.nb_coord=2; MergeData.nb_dim=2; MergeData.dt=1; 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 %-------------------------------------------------------------------------- function MergeData=merge_field(Data) % initiate Matlab structure for physical field if isempty(Data)||~iscell(Data) MergeData=[]; return end MergeData=Data{1};%default error=0; nbview=length(Data); if nbview==1 return end for iview=1:nbview if ~isequal(MergeData.ListDimName,Data{iview}.ListDimName) error=1; end if ~isequal(MergeData.ListVarName,Data{iview}.ListVarName) error=1; end % if ~isequal(MergeData.VarDimIndex,Data{iview}.VarDimIndex) % error=1; % end end if error MergeData.Txt='ERROR: attempt at merging fields of incompatible type'; return end