%'imadoc2struct': reads the xml file for image documentation %------------------------------------------------------------------------ % function [s,errormsg]=imadoc2struct(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(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',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 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); 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