%'ima_levels': rescale the image intensity to reduce strong luminosity peaks (their blinking effects often perturbs PIV)) % this function can be used as a template for applying a transform (here 'levels.m') to each image of a series %------------------------------------------------------------------------ % function GUI_input=ima_levels(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. % %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 ParamOut=ima_levels (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) ParamOut.NbViewMax=1;% max nbre of input file series (default='' , no limitation) 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='off';% 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 = 'off';%can use a transform function ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.lev';%set the output dir extension return end %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% %% 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 ParamOut=Param; %default output if ~isfield(Param,'InputFields') Param.InputFields.FieldName=''; end OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files %% 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); OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files % 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 %not relevant for this function %% check coincidence in time for several input file series %not relevant for this function %% coordinate transform or other user defined transform %not relevant for this function %%%%%%%%%%%% 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 if strcmp(lower(NomType{1}(end)),'a') NomTypeOut=NomType{1}; else NomTypeOut='_1_1'; end else msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image']) return end %% Set field names and velocity types %not relevant for this function %% Initiate output fields %not relevant for this function %% set processing parameters % not needed for this function %% update the xml file % not needed for this function %% main loop on images j1=[];%default for ifile=1:nbfield if checkrun stopstate=get(Param.RUNHandle,'BusyAction'); update_waitbar(Param.WaitbarHandle,ifile/nbfield) else stopstate='queue'; end if isequal(stopstate,'queue') % enable STOP command if ~isempty(j1_series)&&~isequal(j1_series,{[]}) j1=j1_series{1}(ifile); end filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1); A=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); if ndims(A)==3;%color images A=sum(double(Aread),3);% take the sum of color components end % operation on images A=levels(A); filename_new=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); imwrite(A,filename_new) display([filename_new ' written']) end end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function C=levels(A) %whos A; B=double(A(:,:,1)); windowsize=round(min(size(B,1),size(B,2))/20); windowsize=floor(windowsize/2)*2+1; ix=[1/2-windowsize/2:-1/2+windowsize/2];% %del=np/3; %fct=exp(-(ix/del).^2); fct2=cos(ix/(windowsize-1)/2*pi/2); %Mfiltre=(ones(5,5)/5^2); %Mfiltre=fct2'; Mfiltre=fct2'*fct2; Mfiltre=Mfiltre/(sum(sum(Mfiltre))); C=filter2(Mfiltre,B); C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize); C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize); C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:); C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:); C=tanh(B./(2*C)); [n,c]=hist(reshape(C,1,[]),100); % figure;plot(c,n); [m,i]=max(n); c_max=c(i); [dummy,index]=sort(abs(c-c(i))); n=n(index); c=c(index); i_select = find(cumsum(n)<0.95*sum(n)); if isempty(i_select) i_select = 1:length(c); end c_select=c(i_select); n_select=n(i_select); cmin=min(c_select); cmax=max(c_select); C=(C-cmin)/(cmax-cmin)*256; C=uint8(C);