source: trunk/src/series/relabel_i_j.m @ 804

Last change on this file since 804 was 784, checked in by sommeria, 11 years ago

adpat uvmat to reading data from rdvision

File size: 23.3 KB
Line 
1%'relabel_i_j': relabel an image series with two indices, and correct errors from the RDvision transfer program
2%------------------------------------------------------------------------
3% function ParamOut=relabel_i_j(Param)
4%------------------------------------------------------------------------
5%
6%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
7%
8%OUTPUT
9% ParamOut: sets options in the GUI series.fig needed for the function
10%
11%INPUT:
12% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
13% In batch mode, Param is the name of the corresponding xml file containing the same information
14% when Param.Action.RUN=0 (as activated when the current Action is selected
15% in series), the function ouput paramOut set the activation of the needed GUI elements
16%
17% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
18% see the current structure Param)
19%    .InputTable: cell of input file names, (several lines for multiple input)
20%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
21%    .OutputSubDir: name of the subdirectory for data outputs
22%    .OutputDirExt: directory extension for data outputs
23%    .Action: .ActionName: name of the current activated function
24%             .ActionPath:   path of the current activated function
25%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
26%             .RUN =0 for GUI input, =1 for function activation
27%             .RunMode='local','background', 'cluster': type of function  use
28%             
29%    .IndexRange: set the file or frame indices on which the action must be performed
30%    .FieldTransform: .TransformName: name of the selected transform function
31%                     .TransformPath:   path  of the selected transform function
32%    .InputFields: sub structure describing the input fields withfields
33%              .FieldName: name(s) of the field
34%              .VelType: velocity type
35%              .FieldName_1: name of the second field in case of two input series
36%              .VelType_1: velocity type of the second field in case of two input series
37%              .Coord_y: name of y coordinate variable
38%              .Coord_x: name of x coordinate variable
39%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
40%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
41
42function ParamOut=relabel_i_j(Param) %default output=relabel_i_j(Param)
43
44%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
45if isstruct(Param) && isequal(Param.Action.RUN,0)
46    ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
47    ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
48    ParamOut.NbSlice='one'; ...%nbre of slices, 'one' prevents splitting in several processes, ('off' by default)
49    ParamOut.VelType='off';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
50    ParamOut.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
51    ParamOut.FieldTransform = 'off';...%can use a transform function
52    ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on',
53    ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
54    ParamOut.OutputDirExt='';%set the output dir extension
55    if size(Param.InputTable,1)>1
56        msgbox_uvmat('WARNING', 'this function acts only on the first input file line')
57    end
58return
59end
60
61ParamOut=[];
62%%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
63%% read input parameters from an xml file if input is a file name (batch mode)
64checkrun=1;
65if ischar(Param)
66    Param=xml2struct(Param);% read Param as input file (batch case)
67    checkrun=0;
68end
69hseries=findobj(allchild(0),'Tag','series');
70RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
71WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
72
73%% root input file(s) and type
74RootPath=Param.InputTable(:,1);
75RootFile=Param.InputTable(:,3);
76SubDir=Param.InputTable(:,2);
77NomType=Param.InputTable(:,4);
78FileExt=Param.InputTable(:,5);
79
80% get the set of input file names (cell array filecell), and the lists of
81% input file or frame indices i1_series,i2_series,j1_series,j2_series
82[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
83 
84% numbers of slices and file indices
85
86nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
87nbfield_i=size(i1_series{1},2); %nb of fields for the i index
88nbfield=nbfield_j*nbfield_i; %total number of fields
89
90%determine the file type on each line from the first input file
91ImageTypeOptions={'image','multimage','mmreader','video'};
92
93if ~exist(filecell{1,1}','file')
94    msgbox_uvmat('ERROR',['the first input file ' filecell{1,1} ' does not exist'])
95    return
96end
97[FileInfo{1},MovieObject{1}]=get_file_info(filecell{1,1});
98FileType{1}=FileInfo{1}.FileType;
99CheckImage=~isempty(find(strcmp(FileType{1},ImageTypeOptions)));% =1 for images
100
101
102%% calibration data and timing: read the ImaDoc files
103mode=''; %default
104timecell={};
105itime=0;
106NbSlice_calib={};
107
108SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
109filexml=[fullfile(RootPath{1},SubDirBase) '.xml'];%new convention: xml at the level of the image folder
110if ~exist(filexml,'file')
111    filexml=[fullfile(RootPath{1},SubDir{1},RootFile{1}) '.xml']; % old convention: xml inside the image folder
112    if ~exist(filexml,'file')
113        filexml=[fullfile(RootPath{1},SubDir{1},RootFile{1}) '.civ']; % very old convention: .civ file
114        if ~exist(filexml,'file')
115            filexml='';
116        end
117    end
118end
119XmlData=[];
120if ~isempty(filexml)
121    [XmlData,error]=imadoc2struct_special(filexml);
122end
123if isfield(XmlData,'Time')
124    itime=itime+1;
125    timecell{itime}=XmlData.Time;
126end
127if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
128    NbSlice_calib{1}=size(XmlData.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
129    if ~isequal(NbSlice_calib{1},NbSlice_calib{1})
130        msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
131    end
132end
133
134%% check coincidence in time for several input file series
135% not relevant
136
137%% coordinate transform or other user defined transform
138%not relevant
139%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
140 % EDIT FROM HERE
141
142
143%% Set field names and velocity types
144% not relevant here
145
146%% Initiate output fields
147% not relevant here
148
149%% interactive input of specific parameters (for RDvision system)
150display('RDvision system')
151first_label=0; %image numbers start from 0
152if ~CheckImage || ~strcmp(NomType{1},'_000001')
153    msgbox_uvmat('WARNING','the input is not a file from RDvision: this function relabel_i_j has no action');%error message for directory creation
154    return
155else
156    answer=msgbox_uvmat('','this function will relabel the file series from RDvision from  and correct the xml file');%error message for directory creation
157    if ~strcmp(answer,'Yes')
158        return
159    end
160end
161
162%% copy and adapt the xml file
163NomTypeNew='_1_1';
164if ~isempty(XmlData)
165        t=xmltree(filexml);
166       
167        %update information on the first image name in the series
168        uid_Heading=find(t,'ImaDoc/Heading');
169        if isempty(uid_Heading)
170            [t,uid_Heading]=add(t,1,'element','Heading');
171        end
172        uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
173        j1=[];
174        if ~isempty(j1_series{1})
175            j1=j1_series{1};
176        end
177        ImageName=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},'_1_1',i1_series{1}(1),[],j1);
178        [pth,ImageName]=fileparts(ImageName);
179        ImageName=[ImageName '.png'];
180        if isempty(uid_ImageName)
181            [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
182        end
183        uid_value=children(t,uid_ImageName);
184        if isempty(uid_value)
185            t=add(t,uid_ImageName,'chardata',ImageName);%indicate  name of the first image, with ;png extension
186        else
187            t=set(t,uid_value(1),'value',ImageName);%indicate  name of the first image, with ;png extension
188        end
189       
190        %%%% correction RDvision %%%%
191        if isfield(XmlData,'NbDtj')
192            uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
193            uid_value=children(t,uid_NbDtj);
194            if ~isempty(uid_value)
195                t=set(t,uid_value(1),'value',num2str(XmlData.NbDtj));
196            end
197        end
198        if isfield(XmlData,'NbDtk')
199            uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
200            uid_value=children(t,uid_NbDtk);
201            if ~isempty(uid_value)
202                t=set(t,uid_value(1),'value',num2str(XmlData.NbDtk));
203            end
204        end
205        if isempty(j1_series{1}) && isfield(XmlData,'NbDti')
206            uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti');
207            t=add(t,uid_Dti,'chardata',num2str(XmlData.Dti));
208            uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti');
209            t=add(t,uid_NbDti,'chardata',num2str(XmlData.NbDti));
210            uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
211            uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
212            t=delete(t,uid_NbDtj);
213            t=delete(t,uid_NbDtk);
214            uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj');
215            uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk');
216            t=delete(t,uid_Dtj);
217            t=delete(t,uid_Dtk);
218            NomTypeNew='_1';
219        end
220            SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
221    filexml_new=[fullfile(RootPath{1},SubDirBase) '.xml'];
222        save(t,filexml_new)
223end
224
225%% main loop on images
226%j1=[];%default
227nbfield2=1;
228if isfield(XmlData,'Time')
229nbfield2=size(XmlData.Time,2);
230end
231for ifile=1:nbfield
232            update_waitbar(WaitbarHandle,ifile/nbfield)
233    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
234        disp('program stopped by user')
235        break
236    end
237    filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile));
238    j1=[];
239    if ~isequal(nbfield2,1)
240    j1=mod(ifile-1+first_label,nbfield2)+1;
241    end
242    i1=floor((ifile-1+first_label)/nbfield2)+1;
243    filename_new=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomTypeNew,i1,[],j1);
244    try
245        movefile(filename,filename_new);
246        [s,errormsg] = fileattrib(filename_new,'-w','a'); %set images to read only '-w' for all users ('a')
247        if ~s
248            msgbox_uvmat('ERROR',errormsg);
249            return
250        end
251    catch ME
252        msgbox_uvmat('ERROR',ME.message);
253        return
254    end
255   
256end
257
258%'imadoc2struct_special': reads the xml file for image documentation
259%------------------------------------------------------------------------
260% function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
261%
262% OUTPUT:
263% s: structure representing ImaDoc
264%   s.Heading: information about the data hierarchical structure
265%   s.Time: matrix of times
266%   s.TimeUnit
267%  s.GeometryCalib: substructure containing the parameters for geometric calibration
268% errormsg: error message
269%
270% INPUT:
271% ImaDoc: full name of the xml input file with head key ImaDoc
272% option: ='GeometryCalib': read  the data of GeometryCalib, including source point coordinates
273
274function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
275
276%% default input and output
277if ~exist('option','var')
278    option='*';
279end
280errormsg=[];%default
281s.Heading=[];%default
282s.Time=[]; %default
283s.TimeUnit=[]; %default
284s.GeometryCalib=[];
285tsai=[];%default
286
287%% opening the xml file
288if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist
289try
290    t=xmltree(ImaDoc);
291catch
292    errormsg={[ImaDoc ' is not a valid xml file']; lasterr};
293    display(errormsg);
294    return
295end
296uid_root=find(t,'/ImaDoc');
297if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file
298
299
300%% Heading
301uid_Heading=find(t,'/ImaDoc/Heading');
302if ~isempty(uid_Heading),
303    uid_Campaign=find(t,'/ImaDoc/Heading/Campaign');
304    uid_Exp=find(t,'/ImaDoc/Heading/Experiment');
305    uid_Device=find(t,'/ImaDoc/Heading/Device');
306    uid_Record=find(t,'/ImaDoc/Heading/Record');
307    uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName');
308    s.Heading.Campaign=get(t,children(t,uid_Campaign),'value');
309    s.Heading.Experiment=get(t,children(t,uid_Exp),'value');
310    s.Heading.Device=get(t,children(t,uid_Device),'value');
311    if ~isempty(uid_Record)
312        s.Heading.Record=get(t,children(t,uid_Record),'value');
313    end
314    s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value');
315end
316
317%% Camera  and timing
318if strcmp(option,'*') || strcmp(option,'Camera')
319    uid_Camera=find(t,'/ImaDoc/Camera');
320    if ~isempty(uid_Camera)
321        uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize');
322        if ~isempty(uid_ImageSize);
323            ImageSize=get(t,children(t,uid_ImageSize),'value');
324            xindex=findstr(ImageSize,'x');
325            if length(xindex)>=2
326                s.Npx=str2double(ImageSize(1:xindex(1)-1));
327                s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1));
328            end
329        end
330        uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit');
331        if ~isempty(uid_TimeUnit)
332            s.TimeUnit=get(t,children(t,uid_TimeUnit),'value');
333        end
334        uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming');
335        if ~isempty(uid_BurstTiming)
336            for k=1:length(uid_BurstTiming)
337                subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming
338                % reading Dtk
339                Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1);
340                Dtj=get_value(subt,'/BurstTiming/Dtj',[]);
341                Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
342                NbDtj=get_value(subt,'/BurstTiming/NbDtj',[]);
343                %%%% correction RDvision %%%%
344%                 NbDtj=NbDtj/numel(Dtj);
345%                 s.NbDtj=NbDtj;
346%                 %%%%
347                Dti=get_value(subt,'/BurstTiming/Dti',[]);
348                NbDti=get_value(subt,'/BurstTiming/NbDti',1);
349                 %%%% correction RDvision %%%%
350                if isempty(Dti)% series
351                     Dti=Dtj;
352                      NbDti=NbDtj;
353                     Dtj=[];
354                     s.Dti=Dti;
355                     s.NbDti=NbDti;
356                else
357                    % NbDtj=NbDtj/numel(Dtj);%bursts
358                    if ~isempty(NbDtj)
359                    s.NbDtj=NbDtj/numel(Dtj);%bursts;
360                    else
361                        s.NbDtj=1;
362                    end
363                end
364                %%%% %%%%
365                Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
366
367                Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit
368                if ~isempty(Dti)
369                    Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
370                    Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals  Dti
371                end
372                if ~isempty(Dtj)
373                    Dtj=reshape(Dtj'*ones(1,s.NbDtj),1,s.NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
374                    Dtj=[0 Dtj];
375                    Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
376                end
377                % reading Dtk
378                Dtk=get_value(subt,'/BurstTiming/Dtk',[]);
379                NbDtk=get_value(subt,'/BurstTiming/NbDtk',1);
380                %%%% correction RDvision %%%%
381                if ~isequal(NbDtk,1)
382                    NbDtk=-1+(NbDtk+1)/(NbDti+1);
383                end
384                s.NbDtk=NbDtk;
385                %%%%%
386                if isempty(Dtk)
387                    s.Time=[s.Time;Time_val];
388                else
389                    for kblock=1:NbDtk+1
390                        Time_val_k=Time_val+(kblock-1)*Dtk;
391                        s.Time=[s.Time;Time_val_k];
392                    end
393                end
394            end
395        end
396    end
397end
398
399%% motor
400if strcmp(option,'*') || strcmp(option,'GeometryCalib')
401    uid_subtree=find(t,'/ImaDoc/TranslationMotor');
402    if length(uid_subtree)==1
403        subt=branch(t,uid_subtree);%subtree under GeometryCalib
404       [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]);
405    end
406end
407%%  geometric calibration
408if strcmp(option,'*') || strcmp(option,'GeometryCalib')
409    uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib');
410    if ~isempty(uid_GeometryCalib)
411        if length(uid_GeometryCalib)>1
412            errormsg=['More than one GeometryCalib in ' filecivxml];
413            return
414        end
415        subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib
416        cont=get(subt,1,'contents');
417        if ~isempty(cont)
418            uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType');
419            if isequal(length(uid_CalibrationType),1)
420                tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value');
421            end
422            uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit');
423            if isequal(length(uid_CoordUnit),1)
424                tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value');
425            end
426            uid_fx_fy=find(subt,'/GeometryCalib/fx_fy');
427            focal=[];%default fro old convention (Reg Wilson)
428            if isequal(length(uid_fx_fy),1)
429                tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value'));
430            else %old convention (Reg Wilson)
431                uid_focal=find(subt,'/GeometryCalib/focal');
432                uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy');
433                uid_sx=find(subt,'/GeometryCalib/sx');
434                if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx)
435                    dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value'));
436                    sx=str2num(get(subt,children(subt,uid_sx),'value'));
437                    focal=str2num(get(subt,children(subt,uid_focal),'value'));
438                    tsai.fx_fy(1)=sx*focal/dpx_dpy(1);
439                    tsai.fx_fy(2)=focal/dpx_dpy(2);
440                end
441            end
442            uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy');
443            if ~isempty(uid_Cx_Cy)
444                tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value'));
445            end
446            uid_kc=find(subt,'/GeometryCalib/kc');
447            if ~isempty(uid_kc)
448                tsai.kc=str2double(get(subt,children(subt,uid_kc),'value'));
449            else %old convention (Reg Wilson)
450                uid_kappa1=find(subt,'/GeometryCalib/kappa1');
451                if ~isempty(uid_kappa1)&& ~isempty(focal)
452                    kappa1=str2double(get(subt,children(subt,uid_kappa1),'value'));
453                    tsai.kc=-kappa1*focal*focal;
454                end
455            end
456            uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz');
457            if ~isempty(uid_Tx_Ty_Tz)
458                tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value'));
459            end
460            uid_R=find(subt,'/GeometryCalib/R');
461            if ~isempty(uid_R)
462                RR=get(subt,children(subt,uid_R),'value');
463                if length(RR)==3
464                    tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})];
465                end
466            end
467           
468            %look for laser plane definitions
469            uid_Angle=find(subt,'/GeometryCalib/PlaneAngle');
470            uid_Pos=find(subt,'/GeometryCalib/SliceCoord');
471            if isempty(uid_Pos)
472                uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention
473            end
474            if ~isempty(uid_Angle)
475                tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value'));
476            end
477            if ~isempty(uid_Pos)
478                for j=1:length(uid_Pos)
479                    tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value'));
480                end
481                uid_DZ=find(subt,'/GeometryCalib/SliceDZ');
482                uid_NbSlice=find(subt,'/GeometryCalib/NbSlice');
483                if ~isempty(uid_DZ) && ~isempty(uid_NbSlice)
484                    DZ=str2double(get(subt,children(subt,uid_DZ),'value'));
485                    NbSlice=get(subt,children(subt,uid_NbSlice),'value');
486                    if isequal(NbSlice,'volume')
487                        tsai.NbSlice='volume';
488                        NbSlice=NbDtj+1;
489                    else
490                        tsai.NbSlice=str2double(NbSlice);
491                    end
492                    tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1];
493                end
494            end   
495            tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]);
496            tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n');
497            tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]);
498            tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1);
499           
500            if strcmp(option,'GeometryCalib')
501                tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]);
502            end
503            s.GeometryCalib=tsai;
504        end
505    end
506end
507
508%--------------------------------------------------
509%  read a subtree
510% INPUT:
511% t: xltree
512% head_element: head elelemnt of the subtree
513% Data, structure containing
514%    .Key: element name
515%    .Type: type of element ('charg', 'float'....)
516%    .NbOccur: nbre of occurrence, NaN for un specified number
517function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
518%--------------------------------------------------
519s=[];%default
520errormsg='';
521head_element=get(subt,1,'name');
522    cont=get(subt,1,'contents');
523    if ~isempty(cont)
524        for ilist=1:length(Data)
525            uid_key=find(subt,[head_element '/' Data{ilist}]);
526            if ~isequal(length(uid_key),NbOccur(ilist))
527                errormsg=['wrong number of occurence for ' Data{ilist}];
528                return
529            end
530            for ival=1:length(uid_key)
531                val=get(subt,children(subt,uid_key(ival)),'value');
532                if ~NumTest(ilist)
533                    eval(['s.' Data{ilist} '=val;']);
534                else
535                    eval(['s.' Data{ilist} '=str2double(val);'])
536                end
537            end
538        end
539    end
540
541
542%--------------------------------------------------
543%  read an xml element
544function val=get_value(t,label,default)
545%--------------------------------------------------
546val=default;
547uid=find(t,label);%find the element iud(s)
548if ~isempty(uid) %if the element named label exists
549   uid_child=children(t,uid);%find the children
550   if ~isempty(uid_child)
551       data=get(t,uid_child,'type');%get the type of child
552       if iscell(data)% case of multiple element
553           for icell=1:numel(data)
554               val_read=str2num(get(t,uid_child(icell),'value'));
555               if ~isempty(val_read)
556                   val(icell,:)=val_read;
557               end
558           end
559%           val=val';
560       else % case of unique element value
561           val_read=str2num(get(t,uid_child,'value'));
562           if ~isempty(val_read)
563               val=val_read;
564           else
565              val=get(t,uid_child,'value');%char string data
566           end
567       end
568   end
569end
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