%'extract_rdvision': relabel an image series with two indices, and correct errors from the RDvision transfer program %------------------------------------------------------------------------ % function ParamOut=extract_rdvision(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=extract_rdvision(Param) %default output=relabel_i_j(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.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) ParamOut.NbSlice='one'; ...%nbre of slices, 'one' prevents splitting in several processes, ('off' by default) ParamOut.VelType='off';...% 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 = '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.OutputSubDirMode='custom'; %output folder given by the program, not by the GUI series % detect the set of image folder RootPath=Param.InputTable{1,1}; ListStruct=dir(RootPath); ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files ListDir=ListCells(1,find(check_dir & ~check_bad)); % InputTable=cell(numel(ListDir),5); % InputTable(:,2)=ListDir'; isel=0; InputTable=Param.InputTable; for ilist=1:numel(ListDir) ListStructSub=dir(fullfile(RootPath,ListDir{ilist})); ListCellSub=struct2cell(ListStructSub);% transform dir struct to a cell arrray detect_seq=regexp(ListCellSub(1,:),'.seq$'); seq_index=find(~cellfun('isempty',detect_seq),1); if ~isempty(seq_index) % msgbox_uvmat('ERROR',['not seq file in ' ListDir{ilist} ': please check the input folders']) % else isel=isel+1; InputTable{isel,1}=RootPath; InputTable{isel,2}=ListDir{ilist}; RootFile=regexprep(ListCellSub{1,seq_index},'.seq$',''); InputTable{isel,3}=RootFile; InputTable{isel,4}='*'; InputTable{isel,5}='.seq'; end end hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series' hhseries=guidata(hseries); %handles of the elements in 'series' set(hhseries.InputTable,'Data',InputTable) ParamOut.ActionInput.LogPath=RootPath;% indicate the path for the output info: 0_LOG .... return end ParamOut=[]; %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% %% 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 %% root input file(s) and type RootPath=Param.InputTable{1,1}; if ~isempty(find(~strcmp(RootPath,Param.InputTable(:,1))))% if the Rootpath for each camera are not identical disp_uvmat('ERROR','Rootpath for all cameras must be identical',checkrun) return end % 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); %OutputDir=[Param.OutputSubDir Param.OutputDirExt]; % numbers of slices and file indices 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 FileInfo=get_file_info(filecell{1,1}); if strcmp(FileInfo.FileType,'rdvision') if ~isequal(FileInfo.NumberOfFrames,nbfield) msgbox_uvmat('ERROR',['the whole series of ' num2str(FileInfo.NumberOfFrames) ' images must be extracted at once']) %rmfield(OutputDir) return end %% interactive input of specific parameters (for RDvision system) display('converting images from RDvision system...') else msgbox_uvmat('ERROR','the input is not from rdvision: a .seq or .sqb file must be opened') return end t=xmltree; save(t,fullfile(RootPath,'Running.xml'))%create an xml file to indicate that processing takes place %% calibration data and timing: read the ImaDoc files mode=''; %default timecell={}; itime=0; NbSlice_calib={}; %SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.' %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%% loop on the cameras ( #iview) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% for iview=1:size(Param.InputTable,1) filexml=[fullfile(RootPath,Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder if ~exist(filexml,'file') disp_uvmat('ERROR',[filexml ' missing'],checkrun) return end [XmlData,error]=imadoc2struct_special(filexml); if isfield(XmlData,'Time') itime=itime+1; timecell{itime}=XmlData.Time; end if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord') NbSlice_calib{1}=size(XmlData.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform if ~isequal(NbSlice_calib{1},NbSlice_calib{1}) msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); end end % correction to RDvision xml file t=xmltree(filexml); % correct Dtj and Dtk NomTypeNew='_1_1';% new file nomencalture by default ImageName='img_1_1.png';% first image name if isfield(XmlData,'NbDtj') uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); uid_value=children(t,uid_NbDtj); if ~isempty(uid_value) t=set(t,uid_value(1),'value',num2str(XmlData.NbDtj)); end end if isfield(XmlData,'NbDtk') uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); uid_value=children(t,uid_NbDtk); if ~isempty(uid_value) t=set(t,uid_value(1),'value',num2str(XmlData.NbDtk)); end end if isempty(j1_series{1}) && isfield(XmlData,'NbDti') uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti'); t=add(t,uid_Dti,'chardata',num2str(XmlData.Dti)); uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti'); t=add(t,uid_NbDti,'chardata',num2str(XmlData.NbDti)); uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); t=delete(t,uid_NbDtj); t=delete(t,uid_NbDtk); uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj'); uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk'); t=delete(t,uid_Dtj); t=delete(t,uid_Dtk); NomTypeNew='_1'; ImageName='img_1.png'; end %update information of 'Heading' uid_Heading=find(t,'ImaDoc/Heading'); if isempty(uid_Heading) [t,uid_Heading]=add(t,1,'element','Heading'); end uid_SubCampaign=find(t,'ImaDoc/Heading/SubCampaign'); if ~isempty(uid_SubCampaign), t=delete(t,uid_SubCampaign); end uid_Experiment=find(t,'ImaDoc/Heading/Experiment'); if ~isempty(uid_Experiment), t=delete(t,uid_Experiment); end uid_Device=find(t,'ImaDoc/Heading/Device'); if ~isempty(uid_Device), t=delete(t,uid_Device); end uid_Record=find(t,'ImaDoc/Heading/Record'); if ~isempty(uid_Record), t=delete(t,uid_Record); end uid_DateExp=find(t,'ImaDoc/Heading/DateExp'); if ~isempty(uid_DateExp), t=delete(t,uid_DateExp); end %indicate the name of the first image (as a check that the xml file is not moved) uid_ImageName=find(t,'ImaDoc/Heading/ImageName'); if isempty(uid_ImageName) [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); end uid_value=children(t,uid_ImageName); if isempty(uid_value) t=add(t,uid_ImageName,'chardata',ImageName);%indicate name of the first image, with ;png extension else t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension end %indicate the date and time of the image acquisition start % if isfield(FileInfo,'binrepertoire') && isfield(FileInfo,'starttime') % sep_pos=regexp(FileInfo.binrepertoire,'T'); % DateTime=FileInfo.starttime; % if ~isempty(sep_pos) % DateTime=[FileInfo.binrepertoire(1:sep_pos-1) ' ' DateTime]; % end % uid_DateTime=find(t,'ImaDoc/Heading/DateTime'); % if isempty(uid_DateTime) % [t,uid_DateTime]=add(t,uid_Heading,'element','DateTime'); % end % uid_value=children(t,uid_DateTime); % if isempty(uid_value) % t=add(t,uid_DateTime,'chardata',DateTime);%indicate name of the first image, with ;png extension % else % t=set(t,uid_value(1),'value',DateTime);%indicate name of the first image, with ;png extension % end % end %% backup the previous xml file and save the corrected one % [success,message]=copyfile(filexml,[filexml '~']);%make backup % if success~=1 % disp(['errror in xml file backup: ' message]); % return % end save(t,filexml) nbfield2=1; if isfield(XmlData,'Time') nbfield2=size(XmlData.Time,2); end %% get the names of .seq and .sqb files switch Param.InputTable{iview,5} case {'.seq','.sqb'} filename_seq=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.seq']); filename_sqb=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.sqb']); otherwise errormsg='input file extension must be .seq or .sqb'; end if ~exist(filename_seq,'file') errormsg=[filename_seq ' does not exist']; return end %% get data from .seq file s=ini2struct(filename_seq); SeqData=s.sequenceSettings; SeqData.width=str2double(SeqData.width); SeqData.height=str2double(SeqData.height); SeqData.bytesperpixel=str2double(SeqData.bytesperpixel); SeqData.nb_frames=str2double(s.sequenceSettings.numberoffiles); if isempty(SeqData.binrepertoire)%used when binrepertoire empty, strange feature of rdvision SeqData.binrepertoire=regexprep(s.sequenceSettings.bindirectory,'\\$','');%tranform Windows notation to Linux SeqData.binrepertoire=regexprep(SeqData.binrepertoire,'\','/'); [tild,binrepertoire,DirExt]=fileparts(SeqData.binrepertoire); SeqData.binrepertoire=[SeqData.binrepertoire DirExt]; end % PathDir=fileparts(PathDir); %% reading the .sqb file m = memmapfile(filename_sqb,'Format', { 'uint32' [1 1] 'offset'; ... 'uint32' [1 1] 'garbage1';... 'double' [1 1] 'timestamp';... 'uint32' [1 1] 'file_idx';... 'uint32' [1 1] 'garbage2' },'Repeat',SeqData.nb_frames); %%%%%%%BRICOLAGE in case of unreadable .sqb file % ind=[60 63:152];%indices of bin files % lengthimage=w*h*bpp;% lengthof an image record on the binary file % for ii=1:32*numel(ind) % data(ii).offset=mod(ii-1,32)*2*lengthimage+lengthimage;%Dalsa_2 % %data(ii).offset=mod(ii-1,32)*2*lengthimage;%Dalsa_1 % data(ii).file_idx=ind(ceil(ii/32)); % data(ii).timestamp=0.2*(ii-1); % end %%%%%%% for ii=1: numel(m.Data) timestamp(ii)=m.Data(ii).timestamp; end timestamp %todo: check withDt from the xml file [BinSize,errormsg]=binread_rdv_series(RootPath,SeqData,m.Data,nbfield2,NomTypeNew) if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) return end end delete(fullfile(RootPath,'Running.xml'))%delete the xml file to indicate that processing is finished %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %--------- reads a series of bin files %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function [BinSize,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew) % BINREAD_RDV Permet de lire les fichiers bin g�n�r�s par Hiris � partir du % fichier seq associ�. % [IMGS,TIMESTAMPS,NB_FRAMES] = BINREAD_RDV(FILENAME,FRAME_IDX) lit % l'image d'indice FRAME_IDX de la s�quence FILENAME. % % Entr�es % ------- % FILENAME : Nom du fichier s�quence (.seq). % FRAME_IDX : Indice de l'image � lire. Si FRAME_IDX vaut -1 alors la % s�quence est enti�rement lue. Si FRAME_IDX est un tableau d'indices % alors toutes les images d'incides correspondant sont lues. Si FRAME_IDX % est un tableau vide alors aucune image n'est lue mais le nombre % d'images et tous les timestamps sont renvoy�s. Les indices commencent � % 1 et se termines � NB_FRAMES. % % Sorties % ------- % IMGS : Images de sortie. % TIMESTAMPS : Timestaps des images lues. % NB_FRAMES : Nombres d'images dans la s�quence. NbBinFile=0; BinSize=0; fid=0; errormsg=''; classname=sprintf('uint%d',SeqData.bytesperpixel*8); classname=['*' classname]; BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits) binrepertoire=fullfile(PathDir,SeqData.binrepertoire); OutputDir=fullfile(PathDir,SeqData.sequencename); if ~exist(OutputDir,'dir') % errormsg=[OutputDir ' already exist, delete it first']; % return % end [s,errormsg]=mkdir(OutputDir); if s==0 disp(errormsg) return%not able to create new image dir end end for ii=1:SeqData.nb_frames j1=[]; if ~isequal(nbfield2,1) j1=mod(ii-1,nbfield2)+1; end i1=floor((ii-1)/nbfield2)+1; OutputFile=fullfile_uvmat(PathDir,SeqData.sequencename,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx)); if exist(OutputFile,'file') fid=0; else if fid==0 || ~strcmp(fname,fname_prev) % open the bin file if not in use if fid~=0 fclose(fid);%close the previous bin file if relevant end [fid,msg]=fopen(fname,'rb'); if isequal(fid,-1) disp(['error in opening ' fname ': ' msg]) else disp([fname ' opened for reading']) end fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose) BinSize(NbBinFile)=0;% strat counter for new bin file else % fclose(fid);%close the previous bin file % fid=fopen(fname,'rb');% open the new bin file fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file end fname_prev=fname; A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image A=A'; BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read try imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images disp([OutputFile ' written']); % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a') % if ~s % % disp_uvmat('ERROR',errormsg,checkrun); % return % end catch ME errormsg=ME.message; return end end end if fid~=0 fclose(fid) end % for ifile=1:nbfield % update_waitbar(WaitbarHandle,ifile/nbfield) % if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') % disp('program stopped by user') % break % end % [A,FileInfo,timestamps]=read_rdvision(filename,ifile); % if ifile==1 % classA=class(A); % if strcmp(classA,'uint8') % BitDepth=8; % else % BitDepth=16; % end % end % j1=[]; % if ~isequal(nbfield2,1) % j1=mod(ifile-1+first_label,nbfield2)+1; % end % i1=floor((ifile-1+first_label)/nbfield2)+1; % OutputFile=fullfile_uvmat(RootPath{1},OutputDir,'img','.png',NomTypeNew,i1,[],j1); % try % imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images % disp([OutputFile ' written']); % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a') % if ~s % disp_uvmat('ERROR',errormsg,checkrun); % return % end % catch ME % disp_uvmat('ERROR',ME.message,checkrun); % return % end % % end %'imadoc2struct_special': reads the xml file for image documentation %------------------------------------------------------------------------ % function [s,errormsg]=imadoc2struct_special(ImaDoc,option) % % OUTPUT: % s: structure representing ImaDoc % s.Heading: information about the data hierarchical structure % s.Time: matrix of times % s.TimeUnit % s.GeometryCalib: substructure containing the parameters for geometric calibration % errormsg: error message % % INPUT: % ImaDoc: full name of the xml input file with head key ImaDoc % option: ='GeometryCalib': read the data of GeometryCalib, including source point coordinates function [s,errormsg]=imadoc2struct_special(ImaDoc,option) %% default input and output if ~exist('option','var') option='*'; end errormsg=[];%default s.Heading=[];%default s.Time=[]; %default s.TimeUnit=[]; %default s.GeometryCalib=[]; tsai=[];%default %% opening the xml file if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist try t=xmltree(ImaDoc); catch errormsg={[ImaDoc ' is not a valid xml file']; lasterr}; display(errormsg); return end uid_root=find(t,'/ImaDoc'); if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file %% Heading uid_Heading=find(t,'/ImaDoc/Heading'); if ~isempty(uid_Heading), uid_Campaign=find(t,'/ImaDoc/Heading/Campaign'); uid_Exp=find(t,'/ImaDoc/Heading/Experiment'); uid_Device=find(t,'/ImaDoc/Heading/Device'); uid_Record=find(t,'/ImaDoc/Heading/Record'); uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName'); s.Heading.Campaign=get(t,children(t,uid_Campaign),'value'); s.Heading.Experiment=get(t,children(t,uid_Exp),'value'); s.Heading.Device=get(t,children(t,uid_Device),'value'); if ~isempty(uid_Record) s.Heading.Record=get(t,children(t,uid_Record),'value'); end s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value'); end %% Camera and timing if strcmp(option,'*') || strcmp(option,'Camera') uid_Camera=find(t,'/ImaDoc/Camera'); if ~isempty(uid_Camera) uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize'); if ~isempty(uid_ImageSize); ImageSize=get(t,children(t,uid_ImageSize),'value'); xindex=findstr(ImageSize,'x'); if length(xindex)>=2 s.Npx=str2double(ImageSize(1:xindex(1)-1)); s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1)); end end uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit'); if ~isempty(uid_TimeUnit) s.TimeUnit=get(t,children(t,uid_TimeUnit),'value'); end uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming'); if ~isempty(uid_BurstTiming) for k=1:length(uid_BurstTiming) subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming % reading Dtk Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1); Dtj=get_value(subt,'/BurstTiming/Dtj',[]); Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') NbDtj=get_value(subt,'/BurstTiming/NbDtj',[]); %%%% correction RDvision %%%% % NbDtj=NbDtj/numel(Dtj); % s.NbDtj=NbDtj; % %%%% Dti=get_value(subt,'/BurstTiming/Dti',[]); NbDti=get_value(subt,'/BurstTiming/NbDti',1); %%%% correction RDvision %%%% if isempty(Dti)% series Dti=Dtj; NbDti=NbDtj; Dtj=[]; s.Dti=Dti; s.NbDti=NbDti; else % NbDtj=NbDtj/numel(Dtj);%bursts if ~isempty(NbDtj) s.NbDtj=NbDtj/numel(Dtj);%bursts; else s.NbDtj=1; end end %%%% %%%% Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit if ~isempty(Dti) Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals Dti end if ~isempty(Dtj) Dtj=reshape(Dtj'*ones(1,s.NbDtj),1,s.NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times Dtj=[0 Dtj]; Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj end % reading Dtk Dtk=get_value(subt,'/BurstTiming/Dtk',[]); NbDtk=get_value(subt,'/BurstTiming/NbDtk',1); %%%% correction RDvision %%%% if ~isequal(NbDtk,1) NbDtk=-1+(NbDtk+1)/(NbDti+1); end s.NbDtk=NbDtk; %%%%% if isempty(Dtk) s.Time=[s.Time;Time_val]; else for kblock=1:NbDtk+1 Time_val_k=Time_val+(kblock-1)*Dtk; s.Time=[s.Time;Time_val_k]; end end end end end end %% motor if strcmp(option,'*') || strcmp(option,'GeometryCalib') uid_subtree=find(t,'/ImaDoc/TranslationMotor'); if length(uid_subtree)==1 subt=branch(t,uid_subtree);%subtree under GeometryCalib [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]); end end %% geometric calibration if strcmp(option,'*') || strcmp(option,'GeometryCalib') uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib'); if ~isempty(uid_GeometryCalib) if length(uid_GeometryCalib)>1 errormsg=['More than one GeometryCalib in ' filecivxml]; return end subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib cont=get(subt,1,'contents'); if ~isempty(cont) uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType'); if isequal(length(uid_CalibrationType),1) tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value'); end uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit'); if isequal(length(uid_CoordUnit),1) tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value'); end uid_fx_fy=find(subt,'/GeometryCalib/fx_fy'); focal=[];%default fro old convention (Reg Wilson) if isequal(length(uid_fx_fy),1) tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value')); else %old convention (Reg Wilson) uid_focal=find(subt,'/GeometryCalib/focal'); uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy'); uid_sx=find(subt,'/GeometryCalib/sx'); if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx) dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value')); sx=str2num(get(subt,children(subt,uid_sx),'value')); focal=str2num(get(subt,children(subt,uid_focal),'value')); tsai.fx_fy(1)=sx*focal/dpx_dpy(1); tsai.fx_fy(2)=focal/dpx_dpy(2); end end uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy'); if ~isempty(uid_Cx_Cy) tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value')); end uid_kc=find(subt,'/GeometryCalib/kc'); if ~isempty(uid_kc) tsai.kc=str2double(get(subt,children(subt,uid_kc),'value')); else %old convention (Reg Wilson) uid_kappa1=find(subt,'/GeometryCalib/kappa1'); if ~isempty(uid_kappa1)&& ~isempty(focal) kappa1=str2double(get(subt,children(subt,uid_kappa1),'value')); tsai.kc=-kappa1*focal*focal; end end uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz'); if ~isempty(uid_Tx_Ty_Tz) tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value')); end uid_R=find(subt,'/GeometryCalib/R'); if ~isempty(uid_R) RR=get(subt,children(subt,uid_R),'value'); if length(RR)==3 tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})]; end end %look for laser plane definitions uid_Angle=find(subt,'/GeometryCalib/PlaneAngle'); uid_Pos=find(subt,'/GeometryCalib/SliceCoord'); if isempty(uid_Pos) uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention end if ~isempty(uid_Angle) tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value')); end if ~isempty(uid_Pos) for j=1:length(uid_Pos) tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value')); end uid_DZ=find(subt,'/GeometryCalib/SliceDZ'); uid_NbSlice=find(subt,'/GeometryCalib/NbSlice'); if ~isempty(uid_DZ) && ~isempty(uid_NbSlice) DZ=str2double(get(subt,children(subt,uid_DZ),'value')); NbSlice=get(subt,children(subt,uid_NbSlice),'value'); if isequal(NbSlice,'volume') tsai.NbSlice='volume'; NbSlice=NbDtj+1; else tsai.NbSlice=str2double(NbSlice); end tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1]; end end tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]); tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n'); tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]); tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1); if strcmp(option,'GeometryCalib') tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]); end s.GeometryCalib=tsai; end end end %-------------------------------------------------- % read a subtree % INPUT: % t: xltree % head_element: head elelemnt of the subtree % Data, structure containing % .Key: element name % .Type: type of element ('charg', 'float'....) % .NbOccur: nbre of occurrence, NaN for un specified number function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest) %-------------------------------------------------- s=[];%default errormsg=''; head_element=get(subt,1,'name'); cont=get(subt,1,'contents'); if ~isempty(cont) for ilist=1:length(Data) uid_key=find(subt,[head_element '/' Data{ilist}]); if ~isequal(length(uid_key),NbOccur(ilist)) errormsg=['wrong number of occurence for ' Data{ilist}]; return end for ival=1:length(uid_key) val=get(subt,children(subt,uid_key(ival)),'value'); if ~NumTest(ilist) eval(['s.' Data{ilist} '=val;']); else eval(['s.' Data{ilist} '=str2double(val);']) end end end end %-------------------------------------------------- % read an xml element function val=get_value(t,label,default) %-------------------------------------------------- val=default; uid=find(t,label);%find the element iud(s) if ~isempty(uid) %if the element named label exists uid_child=children(t,uid);%find the children if ~isempty(uid_child) data=get(t,uid_child,'type');%get the type of child if iscell(data)% case of multiple element for icell=1:numel(data) val_read=str2num(get(t,uid_child(icell),'value')); if ~isempty(val_read) val(icell,:)=val_read; end end % val=val'; else % case of unique element value val_read=str2num(get(t,uid_child,'value')); if ~isempty(val_read) val=val_read; else val=get(t,uid_child,'value');%char string data end end end end