%'imadoc2struct': reads the xml file for image documentation % %function [s,errormsg]=imadoc2struct(ImaDoc) %-------------------------------------------------------- % 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 %function [s,error,Heading,nom_type_ima,ext_ima,abs_time,TimeUnit,mode,NbSlice]=imadoc2struct(ImaDoc) function [s,errormsg]=imadoc2struct(ImaDoc) errormsg=[];%default s.Heading=[];%default s.Time=[]; %default s.TimeUnit=[]; %default s.GeometryCalib=[]; % nom_type_ima=[];%default % ext_ima=[];%default % abs_time=[];%initiation % GeometryCalib.CoordUnit='cm';%default % mode=[]; %default % NbSlice=1;%default % npx=[];%default % npy=[];%default % GeometryCalib.Pxcmx=1; % GeometryCalib.Pxcmy=1; % GeometryCalib=[]; % NbDtj=1; tsai=[];%default % if ~exist('testime','var') % testime=1;%default 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'); % FirstImage=s.Heading.ImageName; % if ~isempty(FirstImage) % [Pathsub,RootFile,field_count,str2,str_a,str_b,ext,nom_type_ima]=name2display(FirstImage); % end end %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 % npx=str2num(ImageSize(1:xindex(1)-1)); % npy=str2num(ImageSize(xindex(1)+1:xindex(2)-1)); end end % uid_NbSlice=find(t,'/ImaDoc/Camera/NbSlice'); % if ~isempty(uid_NbSlice) % NbSlice=str2num(get(t,children(t,uid_NbSlice),'value')); % % if isempty(NbSlice),NbSlice=1;end; %default % 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) % Dtj=[];%default % NbDtj=1;%default 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',1); Dti=get_value(subt,'/BurstTiming/Dti',[]); Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') NbDti=get_value(subt,'/BurstTiming/NbDti',1); 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,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dti vector NbDti times Dtj=[0 Dtj]; % Time_val' % ones(1,numel(Dtj)) % ones(numel(Time_val'),1) % cumsum(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); if isempty(Dtk) s.Time=[s.Time;Time_val]; else for kblock=1:NbDtk+1 Time_val=Time_val+(kblock-1)*Dtk; s.Time=[s.Time;Time_val]; end end end end if size(s.Time,1)==1 s.Time=(s.Time)'; %change vector into column end end %read calibration 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_pixcmx=find(subt,'/GeometryCalib/Pxcmx'); uid_pixcmy=find(subt,'/GeometryCalib/Pxcmy'); if ~isempty(uid_pixcmx) && ~isempty(uid_pixcmy)%NON UTILISE pixcmx=str2num(get(subt,children(subt,uid_pixcmx),'value')); if isempty(pixcmx),pixcmx=1;end; %default pixcmy=str2num(get(subt,children(subt,uid_pixcmy),'value')); if isempty(pixcmy),pixcmy=1;end; %default tsai.Pxcmx=pixcmx; tsai.Pxcmy=pixcmy; end %default values: tsai.f=1; tsai.dpx=1; tsai.dpy=1; tsai.sx=1; tsai.Cx=0; tsai.Cy=0; tsai.Tz=1; tsai.Tx=0; tsai.Ty=0; tsai.R=[1 0 0; 0 1 0; 0 0 0]; tsai.kappa1=0; uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit'); if ~isempty(uid_CoordUnit) tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value'); end uid_focal=find(subt,'/GeometryCalib/focal'); uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy'); uid_sx=find(subt,'/GeometryCalib/sx'); uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy'); uid_kappa1=find(subt,'/GeometryCalib/kappa1'); uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz'); uid_R=find(subt,'/GeometryCalib/R'); if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_Cx_Cy) tsai.f=str2num(get(subt,children(subt,uid_focal),'value')); dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value')); tsai.dpx=dpx_dpy(1); tsai.dpy=dpx_dpy(2); if ~isempty(uid_sx) tsai.sx=str2num(get(subt,children(subt,uid_sx),'value')); end Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value')); tsai.Cx=Cx_Cy(1); tsai.Cy=Cx_Cy(2); end if ~isempty(uid_Tx_Ty_Tz) Tx_Ty_T_char=get(subt,children(subt,uid_Tx_Ty_Tz),'value'); Tx_Ty_Tz=str2num(Tx_Ty_T_char); tsai.Tx=Tx_Ty_Tz(1); tsai.Ty=Tx_Ty_Tz(2); tsai.Tz=Tx_Ty_Tz(3); end 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 if ~isempty(uid_kappa1) tsai.kappa1=str2num(get(subt,children(subt,uid_kappa1),'value')); end %look for laser plane definitions uid_Angle=find(subt,'/GeometryCalib/PlaneAngle'); uid_Pos=find(subt,'/GeometryCalib/PlanePos'); 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 end s.GeometryCalib=tsai; 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) uid_child=children(t,uid); if ~isempty(uid_child) data=get(t,uid_child,'type'); if iscell(data) 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 val_read=str2num(get(t,uid_child,'value')); if ~isempty(val_read) val=val_read; end end end end