%'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 % varargin: optional list of strings to restrict the reading to a selection of subtrees, for instance 'GeometryCalib' (save time) function [s,errormsg]=imadoc2struct(ImaDoc,varargin) %% default input and output errormsg='';%default s=[]; % s.Heading=[];%default % s.Time=[]; %default % s.TimeUnit=[]; %default % s.GeometryCalib=[]; % tsai=[];%default %% opening the xml file [tild,tild,FileExt]=fileparts(ImaDoc); %% case of .civ files (obsolete) if strcmp(FileExt,'.civ') [errormsg,time,TimeUnit,mode,npx,npy,s.GeometryCalib]=read_imatext(ImaDoc); return end %% case of xml files if nargin ==1 [s,Heading]=xml2struct(ImaDoc);% convert the whole xml file in a structure s elseif nargin ==2 [s,Heading]=xml2struct(ImaDoc,varargin{1});% convert the xml file in a structure s, keeping only the subtree defined in input else %TODO: deal with more than two subtrees? [s,Heading]=xml2struct(ImaDoc,varargin{1},varargin{2});% convert the xml file in a structure s, keeping only the subtree defined in input end if ~strcmp(Heading,'ImaDoc') errormsg='the input xml file is not ImaDoc'; return end %% reading timing if isfield(s,'Camera') Timing=s.Camera.BurstTiming; if ~iscell(Timing) Timing={Timing}; end s.Time=[]; for k=1:length(Timing) Frequency=1; if isfield(Timing{k},'Frequency') Frequency=Timing{k}.FrameFrequency; end Dtj=[]; if isfield(Timing{k},'Dtj') Dtj=Timing{k}.Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's'); end NbDtj=1; if isfield(Timing{k},'NbDtj')&&~isempty(Timing{k}.NbDtj) NbDtj=Timing{k}.NbDtj; end Dti=[]; if isfield(Timing{k},'Dti') Dti=Timing{k}.Dti/Frequency;%Dti converted from frame unit to TimeUnit (e.g. 's'); end NbDti=1; if isfield(Timing{k},'NbDti')&&~isempty(Timing{k}.NbDti) NbDti=Timing{k}.NbDti; end Time_val=Timing{k}.Time;%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=[];%default NbDtk=1;%default if isfield(Timing,'Dtk') Dtk=Timing{k}.Dtk; end if isfield(Timing,'NbDtk')&&~isempty(Timing{k}.NbDtk) NbDtk=Timing{k}.NbDtk; end 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 % try % t=xmltree(ImaDoc); % catch ME % errormsg={['error reading ' ImaDoc ': ']; ME.message}; % display(errormsg); % return % end % uid_root=find(t,'/ImaDoc'); % if isempty(uid_root), 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 %------------------------------------------------------------------------ %'read_imatext': reads the .civ file for image documentation (obsolete) % fileinput: name of the documentation file % time: matrix of times for the set of images %pxcmx: scale along x in pixels/cm %pxcmy: scale along y in pixels/cm function [error,time,TimeUnit,mode,npx,npy,GeometryCalib]=read_imatext(fileinput) %------------------------------------------------------------------------ error='';%default time=[]; %default TimeUnit='s'; mode='pairs'; npx=[]; %default npy=[]; %default GeometryCalib=[]; if ~exist(fileinput,'file'), error=['image doc file ' fileinput ' does not exist']; return;end;%input file does not exist dotciv=textread(fileinput); sizdot=size(dotciv); if ~isequal(sizdot(1)-8,dotciv(1,1)); error=1; %inconsistent number of bursts end nbfield=sizdot(1)-8; npx=(dotciv(2,1)); npy=(dotciv(2,2)); pxcmx=(dotciv(6,1));% pixels/cm in the .civ file pxcmy=(dotciv(6,2)); % nburst=dotciv(3,1); % nbre of bursts abs_time1=dotciv([9:nbfield+8],2); dtime=dotciv(5,1)*(dotciv([9:nbfield+8],[3:end-1])+1); timeshift=[abs_time1 dtime]; time=cumsum(timeshift,2); GeometryCalib.CalibrationType='rescale'; 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';