Index: /trunk/src/imadoc2struct.m =================================================================== --- /trunk/src/imadoc2struct.m (revision 559) +++ /trunk/src/imadoc2struct.m (revision 560) @@ -13,11 +13,8 @@ % 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) +% 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 -if ~exist('option','var') - option='*'; -end errormsg=[];%default s.Heading=[];%default @@ -25,202 +22,271 @@ s.TimeUnit=[]; %default s.GeometryCalib=[]; -tsai=[];%default +% 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 -try - t=xmltree(ImaDoc); -catch ME - errormsg={['error reading ' ImaDoc ': ']; ME.message}; - display(errormsg); + +%% case of xml files +if nargin >1 + [s,Heading]=xml2struct(ImaDoc,varargin);% convert the xml file in a structure s, keeping only the subtree defined in input +else + [s,Heading]=xml2struct(ImaDoc);% convert the whole xml file in a structure s +end +if ~strcmp(Heading,'ImaDoc') + errormsg='the input xml file is not ImaDoc'; 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 +%% reading timing +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') + 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') + 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') + 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 + + +% 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 +% 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 +% 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 +% 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 %-------------------------------------------------- Index: /trunk/src/xml2struct.m =================================================================== --- /trunk/src/xml2struct.m (revision 559) +++ /trunk/src/xml2struct.m (revision 560) @@ -8,10 +8,20 @@ % INPUT: % filename: name of the xml file +% varargin: optional list of strings to restrict the reading to a selection of subtrees, for instance 'GeometryCalib' (save time) -function [s,Heading]=xml2struct(filename) +function [s,Heading]=xml2struct(filename,varargin) t=xmltree(filename); Heading=get(t,1,'name'); -ss=convert(t); -s=convert_string(ss); +if nargin>1 + for isub=1:nargin-1 + uid_sub=find(t,['/' Heading '/' varargin{isub}]); + tsub=branch(t,uid_sub); + ss=convert(tsub); + s.(varargin{isub})=convert_string(ss); + end +else + ss=convert(t); + s=convert_string(ss); +end