source: trunk/src/series/relabel_i_j.m @ 743

Last change on this file since 743 was 736, checked in by sommeria, 11 years ago

various corrections

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[FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1});
98CheckImage=~isempty(find(strcmp(FileType{1},ImageTypeOptions)));% =1 for images
99
100
101%% calibration data and timing: read the ImaDoc files
102mode=''; %default
103timecell={};
104itime=0;
105NbSlice_calib={};
106
107SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
108filexml=[fullfile(RootPath{1},SubDirBase) '.xml'];%new convention: xml at the level of the image folder
109if ~exist(filexml,'file')
110    filexml=[fullfile(RootPath{1},SubDir{1},RootFile{1}) '.xml']; % old convention: xml inside the image folder
111    if ~exist(filexml,'file')
112        filexml=[fullfile(RootPath{1},SubDir{1},RootFile{1}) '.civ']; % very old convention: .civ file
113        if ~exist(filexml,'file')
114            filexml='';
115        end
116    end
117end
118XmlData=[];
119if ~isempty(filexml)
120    [XmlData,error]=imadoc2struct_special(filexml);
121end
122if isfield(XmlData,'Time')
123    itime=itime+1;
124    timecell{itime}=XmlData.Time;
125end
126if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
127    NbSlice_calib{1}=size(XmlData.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
128    if ~isequal(NbSlice_calib{1},NbSlice_calib{1})
129        msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
130    end
131end
132
133%% check coincidence in time for several input file series
134% not relevant
135
136%% coordinate transform or other user defined transform
137%not relevant
138%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
139 % EDIT FROM HERE
140
141
142%% Set field names and velocity types
143% not relevant here
144
145%% Initiate output fields
146% not relevant here
147
148%% interactive input of specific parameters (for RDvision system)
149display('RDvision system')
150first_label=0; %image numbers start from 0
151if ~CheckImage || ~strcmp(NomType{1},'_000001')
152    msgbox_uvmat('WARNING','the input is not a file from RDvision: this function relabel_i_j has no action');%error message for directory creation
153    return
154else
155    answer=msgbox_uvmat('','this function will relabel the file series from RDvision from  and correct the xml file');%error message for directory creation
156    if ~strcmp(answer,'Yes')
157        return
158    end
159end
160
161%% copy and adapt the xml file
162NomTypeNew='_1_1';
163if ~isempty(XmlData)
164        t=xmltree(filexml);
165       
166        %update information on the first image name in the series
167        uid_Heading=find(t,'ImaDoc/Heading');
168        if isempty(uid_Heading)
169            [t,uid_Heading]=add(t,1,'element','Heading');
170        end
171        uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
172        j1=[];
173        if ~isempty(j1_series{1})
174            j1=j1_series{1};
175        end
176        ImageName=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},'_1_1',i1_series{1}(1),[],j1);
177        [pth,ImageName]=fileparts(ImageName);
178        ImageName=[ImageName '.png'];
179        if isempty(uid_ImageName)
180            [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
181        end
182        uid_value=children(t,uid_ImageName);
183        if isempty(uid_value)
184            t=add(t,uid_ImageName,'chardata',ImageName);%indicate  name of the first image, with ;png extension
185        else
186            t=set(t,uid_value(1),'value',ImageName);%indicate  name of the first image, with ;png extension
187        end
188       
189        %%%% correction RDvision %%%%
190        if isfield(XmlData,'NbDtj')
191            uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
192            uid_value=children(t,uid_NbDtj);
193            if ~isempty(uid_value)
194                t=set(t,uid_value(1),'value',num2str(XmlData.NbDtj));
195            end
196        end
197        if isfield(XmlData,'NbDtk')
198            uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
199            uid_value=children(t,uid_NbDtk);
200            if ~isempty(uid_value)
201                t=set(t,uid_value(1),'value',num2str(XmlData.NbDtk));
202            end
203        end
204        if isempty(j1_series{1}) && isfield(XmlData,'NbDti')
205            uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti');
206            t=add(t,uid_Dti,'chardata',num2str(XmlData.Dti));
207            uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti');
208            t=add(t,uid_NbDti,'chardata',num2str(XmlData.NbDti));
209            uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
210            uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
211            t=delete(t,uid_NbDtj);
212            t=delete(t,uid_NbDtk);
213            uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj');
214            uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk');
215            t=delete(t,uid_Dtj);
216            t=delete(t,uid_Dtk);
217            NomTypeNew='_1';
218        end
219            SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
220    filexml_new=[fullfile(RootPath{1},SubDirBase) '.xml'];
221        save(t,filexml_new)
222end
223
224%% main loop on images
225%j1=[];%default
226nbfield2=1;
227if isfield(XmlData,'Time')
228nbfield2=size(XmlData.Time,2);
229end
230for ifile=1:nbfield
231            update_waitbar(WaitbarHandle,ifile/nbfield)
232    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
233        disp('program stopped by user')
234        break
235    end
236    filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile));
237    j1=[];
238    if ~isequal(nbfield2,1)
239    j1=mod(ifile-1+first_label,nbfield2)+1;
240    end
241    i1=floor((ifile-1+first_label)/nbfield2)+1;
242    filename_new=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomTypeNew,i1,[],j1);
243    try
244        movefile(filename,filename_new);
245        [s,errormsg] = fileattrib(filename_new,'-w','a'); %set images to read only '-w' for all users ('a')
246        if ~s
247            msgbox_uvmat('ERROR',errormsg);
248            return
249        end
250    catch ME
251        msgbox_uvmat('ERROR',ME.message);
252        return
253    end
254   
255end
256
257%'imadoc2struct_special': reads the xml file for image documentation
258%------------------------------------------------------------------------
259% function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
260%
261% OUTPUT:
262% s: structure representing ImaDoc
263%   s.Heading: information about the data hierarchical structure
264%   s.Time: matrix of times
265%   s.TimeUnit
266%  s.GeometryCalib: substructure containing the parameters for geometric calibration
267% errormsg: error message
268%
269% INPUT:
270% ImaDoc: full name of the xml input file with head key ImaDoc
271% option: ='GeometryCalib': read  the data of GeometryCalib, including source point coordinates
272
273function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
274
275%% default input and output
276if ~exist('option','var')
277    option='*';
278end
279errormsg=[];%default
280s.Heading=[];%default
281s.Time=[]; %default
282s.TimeUnit=[]; %default
283s.GeometryCalib=[];
284tsai=[];%default
285
286%% opening the xml file
287if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist
288try
289    t=xmltree(ImaDoc);
290catch
291    errormsg={[ImaDoc ' is not a valid xml file']; lasterr};
292    display(errormsg);
293    return
294end
295uid_root=find(t,'/ImaDoc');
296if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file
297
298
299%% Heading
300uid_Heading=find(t,'/ImaDoc/Heading');
301if ~isempty(uid_Heading),
302    uid_Campaign=find(t,'/ImaDoc/Heading/Campaign');
303    uid_Exp=find(t,'/ImaDoc/Heading/Experiment');
304    uid_Device=find(t,'/ImaDoc/Heading/Device');
305    uid_Record=find(t,'/ImaDoc/Heading/Record');
306    uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName');
307    s.Heading.Campaign=get(t,children(t,uid_Campaign),'value');
308    s.Heading.Experiment=get(t,children(t,uid_Exp),'value');
309    s.Heading.Device=get(t,children(t,uid_Device),'value');
310    if ~isempty(uid_Record)
311        s.Heading.Record=get(t,children(t,uid_Record),'value');
312    end
313    s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value');
314end
315
316%% Camera  and timing
317if strcmp(option,'*') || strcmp(option,'Camera')
318    uid_Camera=find(t,'/ImaDoc/Camera');
319    if ~isempty(uid_Camera)
320        uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize');
321        if ~isempty(uid_ImageSize);
322            ImageSize=get(t,children(t,uid_ImageSize),'value');
323            xindex=findstr(ImageSize,'x');
324            if length(xindex)>=2
325                s.Npx=str2double(ImageSize(1:xindex(1)-1));
326                s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1));
327            end
328        end
329        uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit');
330        if ~isempty(uid_TimeUnit)
331            s.TimeUnit=get(t,children(t,uid_TimeUnit),'value');
332        end
333        uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming');
334        if ~isempty(uid_BurstTiming)
335            for k=1:length(uid_BurstTiming)
336                subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming
337                % reading Dtk
338                Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1);
339                Dtj=get_value(subt,'/BurstTiming/Dtj',[]);
340                Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
341                NbDtj=get_value(subt,'/BurstTiming/NbDtj',[]);
342                %%%% correction RDvision %%%%
343%                 NbDtj=NbDtj/numel(Dtj);
344%                 s.NbDtj=NbDtj;
345%                 %%%%
346                Dti=get_value(subt,'/BurstTiming/Dti',[]);
347                NbDti=get_value(subt,'/BurstTiming/NbDti',1);
348                 %%%% correction RDvision %%%%
349                if isempty(Dti)% series
350                     Dti=Dtj;
351                      NbDti=NbDtj;
352                     Dtj=[];
353                     s.Dti=Dti;
354                     s.NbDti=NbDti;
355                else
356                    % NbDtj=NbDtj/numel(Dtj);%bursts
357                    if ~isempty(NbDtj)
358                    s.NbDtj=NbDtj/numel(Dtj);%bursts;
359                    else
360                        s.NbDtj=1;
361                    end
362                end
363                %%%% %%%%
364                Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
365
366                Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit
367                if ~isempty(Dti)
368                    Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
369                    Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals  Dti
370                end
371                if ~isempty(Dtj)
372                    Dtj=reshape(Dtj'*ones(1,s.NbDtj),1,s.NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
373                    Dtj=[0 Dtj];
374                    Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
375                end
376                % reading Dtk
377                Dtk=get_value(subt,'/BurstTiming/Dtk',[]);
378                NbDtk=get_value(subt,'/BurstTiming/NbDtk',1);
379                %%%% correction RDvision %%%%
380                if ~isequal(NbDtk,1)
381                    NbDtk=-1+(NbDtk+1)/(NbDti+1);
382                end
383                s.NbDtk=NbDtk;
384                %%%%%
385                if isempty(Dtk)
386                    s.Time=[s.Time;Time_val];
387                else
388                    for kblock=1:NbDtk+1
389                        Time_val_k=Time_val+(kblock-1)*Dtk;
390                        s.Time=[s.Time;Time_val_k];
391                    end
392                end
393            end
394        end
395    end
396end
397
398%% motor
399if strcmp(option,'*') || strcmp(option,'GeometryCalib')
400    uid_subtree=find(t,'/ImaDoc/TranslationMotor');
401    if length(uid_subtree)==1
402        subt=branch(t,uid_subtree);%subtree under GeometryCalib
403       [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]);
404    end
405end
406%%  geometric calibration
407if strcmp(option,'*') || strcmp(option,'GeometryCalib')
408    uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib');
409    if ~isempty(uid_GeometryCalib)
410        if length(uid_GeometryCalib)>1
411            errormsg=['More than one GeometryCalib in ' filecivxml];
412            return
413        end
414        subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib
415        cont=get(subt,1,'contents');
416        if ~isempty(cont)
417            uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType');
418            if isequal(length(uid_CalibrationType),1)
419                tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value');
420            end
421            uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit');
422            if isequal(length(uid_CoordUnit),1)
423                tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value');
424            end
425            uid_fx_fy=find(subt,'/GeometryCalib/fx_fy');
426            focal=[];%default fro old convention (Reg Wilson)
427            if isequal(length(uid_fx_fy),1)
428                tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value'));
429            else %old convention (Reg Wilson)
430                uid_focal=find(subt,'/GeometryCalib/focal');
431                uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy');
432                uid_sx=find(subt,'/GeometryCalib/sx');
433                if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx)
434                    dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value'));
435                    sx=str2num(get(subt,children(subt,uid_sx),'value'));
436                    focal=str2num(get(subt,children(subt,uid_focal),'value'));
437                    tsai.fx_fy(1)=sx*focal/dpx_dpy(1);
438                    tsai.fx_fy(2)=focal/dpx_dpy(2);
439                end
440            end
441            uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy');
442            if ~isempty(uid_Cx_Cy)
443                tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value'));
444            end
445            uid_kc=find(subt,'/GeometryCalib/kc');
446            if ~isempty(uid_kc)
447                tsai.kc=str2double(get(subt,children(subt,uid_kc),'value'));
448            else %old convention (Reg Wilson)
449                uid_kappa1=find(subt,'/GeometryCalib/kappa1');
450                if ~isempty(uid_kappa1)&& ~isempty(focal)
451                    kappa1=str2double(get(subt,children(subt,uid_kappa1),'value'));
452                    tsai.kc=-kappa1*focal*focal;
453                end
454            end
455            uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz');
456            if ~isempty(uid_Tx_Ty_Tz)
457                tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value'));
458            end
459            uid_R=find(subt,'/GeometryCalib/R');
460            if ~isempty(uid_R)
461                RR=get(subt,children(subt,uid_R),'value');
462                if length(RR)==3
463                    tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})];
464                end
465            end
466           
467            %look for laser plane definitions
468            uid_Angle=find(subt,'/GeometryCalib/PlaneAngle');
469            uid_Pos=find(subt,'/GeometryCalib/SliceCoord');
470            if isempty(uid_Pos)
471                uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention
472            end
473            if ~isempty(uid_Angle)
474                tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value'));
475            end
476            if ~isempty(uid_Pos)
477                for j=1:length(uid_Pos)
478                    tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value'));
479                end
480                uid_DZ=find(subt,'/GeometryCalib/SliceDZ');
481                uid_NbSlice=find(subt,'/GeometryCalib/NbSlice');
482                if ~isempty(uid_DZ) && ~isempty(uid_NbSlice)
483                    DZ=str2double(get(subt,children(subt,uid_DZ),'value'));
484                    NbSlice=get(subt,children(subt,uid_NbSlice),'value');
485                    if isequal(NbSlice,'volume')
486                        tsai.NbSlice='volume';
487                        NbSlice=NbDtj+1;
488                    else
489                        tsai.NbSlice=str2double(NbSlice);
490                    end
491                    tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1];
492                end
493            end   
494            tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]);
495            tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n');
496            tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]);
497            tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1);
498           
499            if strcmp(option,'GeometryCalib')
500                tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]);
501            end
502            s.GeometryCalib=tsai;
503        end
504    end
505end
506
507%--------------------------------------------------
508%  read a subtree
509% INPUT:
510% t: xltree
511% head_element: head elelemnt of the subtree
512% Data, structure containing
513%    .Key: element name
514%    .Type: type of element ('charg', 'float'....)
515%    .NbOccur: nbre of occurrence, NaN for un specified number
516function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
517%--------------------------------------------------
518s=[];%default
519errormsg='';
520head_element=get(subt,1,'name');
521    cont=get(subt,1,'contents');
522    if ~isempty(cont)
523        for ilist=1:length(Data)
524            uid_key=find(subt,[head_element '/' Data{ilist}]);
525            if ~isequal(length(uid_key),NbOccur(ilist))
526                errormsg=['wrong number of occurence for ' Data{ilist}];
527                return
528            end
529            for ival=1:length(uid_key)
530                val=get(subt,children(subt,uid_key(ival)),'value');
531                if ~NumTest(ilist)
532                    eval(['s.' Data{ilist} '=val;']);
533                else
534                    eval(['s.' Data{ilist} '=str2double(val);'])
535                end
536            end
537        end
538    end
539
540
541%--------------------------------------------------
542%  read an xml element
543function val=get_value(t,label,default)
544%--------------------------------------------------
545val=default;
546uid=find(t,label);%find the element iud(s)
547if ~isempty(uid) %if the element named label exists
548   uid_child=children(t,uid);%find the children
549   if ~isempty(uid_child)
550       data=get(t,uid_child,'type');%get the type of child
551       if iscell(data)% case of multiple element
552           for icell=1:numel(data)
553               val_read=str2num(get(t,uid_child(icell),'value'));
554               if ~isempty(val_read)
555                   val(icell,:)=val_read;
556               end
557           end
558%           val=val';
559       else % case of unique element value
560           val_read=str2num(get(t,uid_child,'value'));
561           if ~isempty(val_read)
562               val=val_read;
563           else
564              val=get(t,uid_child,'value');%char string data
565           end
566       end
567   end
568end
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