Changeset 675 for trunk/src/imadoc2struct.m

Timestamp:

Aug 27, 2013, 11:25:21 PM (11 years ago)

Author:

sommeria

Message:

various bugs corrected

File:

• trunk/src/imadoc2struct.m (modified) (2 diffs)

trunk/src/imadoc2struct.m

@@ -47 +47 @@
 %% reading timing
 if isfield(s,'Camera')
+    if isfield(s.Camera,'TimeUnit')
+        s.TimeUnit=s.Camera.TimeUnit;
+    end
     Timing=s.Camera.BurstTiming;
     if ~iscell(Timing)
@@ -105 +108 @@
 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)
 %--------------------------------------------------