source: trunk/src/series/usr_fct/relabel_i_j.m @ 1061

Last change on this file since 1061 was 1061, checked in by g7moreau, 2 years ago
  • Update copyright to year 2019
File size: 24.2 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
42%=======================================================================
43% Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
44%   http://www.legi.grenoble-inp.fr
45%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
46%
47%     This file is part of the toolbox UVMAT.
48%
49%     UVMAT is free software; you can redistribute it and/or modify
50%     it under the terms of the GNU General Public License as published
51%     by the Free Software Foundation; either version 2 of the license,
52%     or (at your option) any later version.
53%
54%     UVMAT is distributed in the hope that it will be useful,
55%     but WITHOUT ANY WARRANTY; without even the implied warranty of
56%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
57%     GNU General Public License (see LICENSE.txt) for more details.
58%=======================================================================
59
60function ParamOut=relabel_i_j(Param) %default output=relabel_i_j(Param)
61
62%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
63if isstruct(Param) && isequal(Param.Action.RUN,0)
64    ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
65    ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
66    ParamOut.NbSlice='one'; ...%nbre of slices, 'one' prevents splitting in several processes, ('off' by default)
67    ParamOut.VelType='off';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
68    ParamOut.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
69    ParamOut.FieldTransform = 'off';...%can use a transform function
70    ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on',
71    ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
72    ParamOut.OutputDirExt='';%set the output dir extension
73    if size(Param.InputTable,1)>1
74        msgbox_uvmat('WARNING', 'this function acts only on the first input file line')
75    end
76return
77end
78
79ParamOut=[];
80%%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
81%% read input parameters from an xml file if input is a file name (batch mode)
82checkrun=1;
83if ischar(Param)
84    Param=xml2struct(Param);% read Param as input file (batch case)
85    checkrun=0;
86end
87hseries=findobj(allchild(0),'Tag','series');
88RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
89WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
90
91%% root input file(s) and type
92RootPath=Param.InputTable(:,1);
93RootFile=Param.InputTable(:,3);
94SubDir=Param.InputTable(:,2);
95NomType=Param.InputTable(:,4);
96FileExt=Param.InputTable(:,5);
97
98% get the set of input file names (cell array filecell), and the lists of
99% input file or frame indices i1_series,i2_series,j1_series,j2_series
100[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
101 
102% numbers of slices and file indices
103
104nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
105nbfield_i=size(i1_series{1},2); %nb of fields for the i index
106nbfield=nbfield_j*nbfield_i; %total number of fields
107
108%determine the file type on each line from the first input file
109ImageTypeOptions={'image','multimage','mmreader','video'};
110
111if ~exist(filecell{1,1}','file')
112    msgbox_uvmat('ERROR',['the first input file ' filecell{1,1} ' does not exist'])
113    return
114end
115[FileInfo{1},MovieObject{1}]=get_file_info(filecell{1,1});
116FileType{1}=FileInfo{1}.FileType;
117CheckImage=~isempty(find(strcmp(FileType{1},ImageTypeOptions)));% =1 for images
118
119
120%% calibration data and timing: read the ImaDoc files
121mode=''; %default
122timecell={};
123itime=0;
124NbSlice_calib={};
125
126SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
127filexml=[fullfile(RootPath{1},SubDirBase) '.xml'];%new convention: xml at the level of the image folder
128if ~exist(filexml,'file')
129    filexml=[fullfile(RootPath{1},SubDir{1},RootFile{1}) '.xml']; % old convention: xml inside the image folder
130    if ~exist(filexml,'file')
131        filexml=[fullfile(RootPath{1},SubDir{1},RootFile{1}) '.civ']; % very old convention: .civ file
132        if ~exist(filexml,'file')
133            filexml='';
134        end
135    end
136end
137XmlData=[];
138if ~isempty(filexml)
139    [XmlData,error]=imadoc2struct_special(filexml);
140end
141if isfield(XmlData,'Time')
142    itime=itime+1;
143    timecell{itime}=XmlData.Time;
144end
145if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
146    NbSlice_calib{1}=size(XmlData.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
147    if ~isequal(NbSlice_calib{1},NbSlice_calib{1})
148        msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
149    end
150end
151
152%% check coincidence in time for several input file series
153% not relevant
154
155%% coordinate transform or other user defined transform
156%not relevant
157%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
158 % EDIT FROM HERE
159
160
161%% Set field names and velocity types
162% not relevant here
163
164%% Initiate output fields
165% not relevant here
166
167%% interactive input of specific parameters (for RDvision system)
168display('RDvision system')
169first_label=0; %image numbers start from 0
170if ~CheckImage || ~strcmp(NomType{1},'_000001')
171    msgbox_uvmat('WARNING','the input is not a file from RDvision: this function relabel_i_j has no action');%error message for directory creation
172    return
173else
174    answer=msgbox_uvmat('','this function will relabel the file series from RDvision from  and correct the xml file');%error message for directory creation
175    if ~strcmp(answer,'Yes')
176        return
177    end
178end
179
180%% copy and adapt the xml file
181NomTypeNew='_1_1';
182if ~isempty(XmlData)
183        t=xmltree(filexml);
184       
185        %update information on the first image name in the series
186        uid_Heading=find(t,'ImaDoc/Heading');
187        if isempty(uid_Heading)
188            [t,uid_Heading]=add(t,1,'element','Heading');
189        end
190        uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
191        j1=[];
192        if ~isempty(j1_series{1})
193            j1=j1_series{1};
194        end
195        ImageName=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},'_1_1',i1_series{1}(1),[],j1);
196        [pth,ImageName]=fileparts(ImageName);
197        ImageName=[ImageName '.png'];
198        if isempty(uid_ImageName)
199            [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
200        end
201        uid_value=children(t,uid_ImageName);
202        if isempty(uid_value)
203            t=add(t,uid_ImageName,'chardata',ImageName);%indicate  name of the first image, with ;png extension
204        else
205            t=set(t,uid_value(1),'value',ImageName);%indicate  name of the first image, with ;png extension
206        end
207       
208        %%%% correction RDvision %%%%
209        if isfield(XmlData,'NbDtj')
210            uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
211            uid_value=children(t,uid_NbDtj);
212            if ~isempty(uid_value)
213                t=set(t,uid_value(1),'value',num2str(XmlData.NbDtj));
214            end
215        end
216        if isfield(XmlData,'NbDtk')
217            uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
218            uid_value=children(t,uid_NbDtk);
219            if ~isempty(uid_value)
220                t=set(t,uid_value(1),'value',num2str(XmlData.NbDtk));
221            end
222        end
223        if isempty(j1_series{1}) && isfield(XmlData,'NbDti')
224            uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti');
225            t=add(t,uid_Dti,'chardata',num2str(XmlData.Dti));
226            uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti');
227            t=add(t,uid_NbDti,'chardata',num2str(XmlData.NbDti));
228            uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
229            uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
230            t=delete(t,uid_NbDtj);
231            t=delete(t,uid_NbDtk);
232            uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj');
233            uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk');
234            t=delete(t,uid_Dtj);
235            t=delete(t,uid_Dtk);
236            NomTypeNew='_1';
237        end
238            SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
239    filexml_new=[fullfile(RootPath{1},SubDirBase) '.xml'];
240        save(t,filexml_new)
241end
242
243%% main loop on images
244%j1=[];%default
245nbfield2=1;
246if isfield(XmlData,'Time')
247nbfield2=size(XmlData.Time,2);
248end
249for ifile=1:nbfield
250            update_waitbar(WaitbarHandle,ifile/nbfield)
251    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
252        disp('program stopped by user')
253        break
254    end
255    filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile));
256    j1=[];
257    if ~isequal(nbfield2,1)
258    j1=mod(ifile-1+first_label,nbfield2)+1;
259    end
260    i1=floor((ifile-1+first_label)/nbfield2)+1;
261    filename_new=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomTypeNew,i1,[],j1);
262    try
263        movefile(filename,filename_new);
264        [s,errormsg] = fileattrib(filename_new,'-w','a'); %set images to read only '-w' for all users ('a')
265        if ~s
266            msgbox_uvmat('ERROR',errormsg);
267            return
268        end
269    catch ME
270        msgbox_uvmat('ERROR',ME.message);
271        return
272    end
273   
274end
275
276%'imadoc2struct_special': reads the xml file for image documentation
277%------------------------------------------------------------------------
278% function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
279%
280% OUTPUT:
281% s: structure representing ImaDoc
282%   s.Heading: information about the data hierarchical structure
283%   s.Time: matrix of times
284%   s.TimeUnit
285%  s.GeometryCalib: substructure containing the parameters for geometric calibration
286% errormsg: error message
287%
288% INPUT:
289% ImaDoc: full name of the xml input file with head key ImaDoc
290% option: ='GeometryCalib': read  the data of GeometryCalib, including source point coordinates
291
292function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
293
294%% default input and output
295if ~exist('option','var')
296    option='*';
297end
298errormsg=[];%default
299s.Heading=[];%default
300s.Time=[]; %default
301s.TimeUnit=[]; %default
302s.GeometryCalib=[];
303tsai=[];%default
304
305%% opening the xml file
306if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist
307try
308    t=xmltree(ImaDoc);
309catch
310    errormsg={[ImaDoc ' is not a valid xml file']; lasterr};
311    display(errormsg);
312    return
313end
314uid_root=find(t,'/ImaDoc');
315if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file
316
317
318%% Heading
319uid_Heading=find(t,'/ImaDoc/Heading');
320if ~isempty(uid_Heading),
321    uid_Campaign=find(t,'/ImaDoc/Heading/Campaign');
322    uid_Exp=find(t,'/ImaDoc/Heading/Experiment');
323    uid_Device=find(t,'/ImaDoc/Heading/Device');
324    uid_Record=find(t,'/ImaDoc/Heading/Record');
325    uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName');
326    s.Heading.Campaign=get(t,children(t,uid_Campaign),'value');
327    s.Heading.Experiment=get(t,children(t,uid_Exp),'value');
328    s.Heading.Device=get(t,children(t,uid_Device),'value');
329    if ~isempty(uid_Record)
330        s.Heading.Record=get(t,children(t,uid_Record),'value');
331    end
332    s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value');
333end
334
335%% Camera  and timing
336if strcmp(option,'*') || strcmp(option,'Camera')
337    uid_Camera=find(t,'/ImaDoc/Camera');
338    if ~isempty(uid_Camera)
339        uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize');
340        if ~isempty(uid_ImageSize);
341            ImageSize=get(t,children(t,uid_ImageSize),'value');
342            xindex=findstr(ImageSize,'x');
343            if length(xindex)>=2
344                s.Npx=str2double(ImageSize(1:xindex(1)-1));
345                s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1));
346            end
347        end
348        uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit');
349        if ~isempty(uid_TimeUnit)
350            s.TimeUnit=get(t,children(t,uid_TimeUnit),'value');
351        end
352        uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming');
353        if ~isempty(uid_BurstTiming)
354            for k=1:length(uid_BurstTiming)
355                subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming
356                % reading Dtk
357                Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1);
358                Dtj=get_value(subt,'/BurstTiming/Dtj',[]);
359                Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
360                NbDtj=get_value(subt,'/BurstTiming/NbDtj',[]);
361                %%%% correction RDvision %%%%
362%                 NbDtj=NbDtj/numel(Dtj);
363%                 s.NbDtj=NbDtj;
364%                 %%%%
365                Dti=get_value(subt,'/BurstTiming/Dti',[]);
366                NbDti=get_value(subt,'/BurstTiming/NbDti',1);
367                 %%%% correction RDvision %%%%
368                if isempty(Dti)% series
369                     Dti=Dtj;
370                      NbDti=NbDtj;
371                     Dtj=[];
372                     s.Dti=Dti;
373                     s.NbDti=NbDti;
374                else
375                    % NbDtj=NbDtj/numel(Dtj);%bursts
376                    if ~isempty(NbDtj)
377                    s.NbDtj=NbDtj/numel(Dtj);%bursts;
378                    else
379                        s.NbDtj=1;
380                    end
381                end
382                %%%% %%%%
383                Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
384
385                Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit
386                if ~isempty(Dti)
387                    Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
388                    Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals  Dti
389                end
390                if ~isempty(Dtj)
391                    Dtj=reshape(Dtj'*ones(1,s.NbDtj),1,s.NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
392                    Dtj=[0 Dtj];
393                    Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
394                end
395                % reading Dtk
396                Dtk=get_value(subt,'/BurstTiming/Dtk',[]);
397                NbDtk=get_value(subt,'/BurstTiming/NbDtk',1);
398                %%%% correction RDvision %%%%
399                if ~isequal(NbDtk,1)
400                    NbDtk=-1+(NbDtk+1)/(NbDti+1);
401                end
402                s.NbDtk=NbDtk;
403                %%%%%
404                if isempty(Dtk)
405                    s.Time=[s.Time;Time_val];
406                else
407                    for kblock=1:NbDtk+1
408                        Time_val_k=Time_val+(kblock-1)*Dtk;
409                        s.Time=[s.Time;Time_val_k];
410                    end
411                end
412            end
413        end
414    end
415end
416
417%% motor
418if strcmp(option,'*') || strcmp(option,'GeometryCalib')
419    uid_subtree=find(t,'/ImaDoc/TranslationMotor');
420    if length(uid_subtree)==1
421        subt=branch(t,uid_subtree);%subtree under GeometryCalib
422       [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]);
423    end
424end
425%%  geometric calibration
426if strcmp(option,'*') || strcmp(option,'GeometryCalib')
427    uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib');
428    if ~isempty(uid_GeometryCalib)
429        if length(uid_GeometryCalib)>1
430            errormsg=['More than one GeometryCalib in ' filecivxml];
431            return
432        end
433        subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib
434        cont=get(subt,1,'contents');
435        if ~isempty(cont)
436            uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType');
437            if isequal(length(uid_CalibrationType),1)
438                tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value');
439            end
440            uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit');
441            if isequal(length(uid_CoordUnit),1)
442                tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value');
443            end
444            uid_fx_fy=find(subt,'/GeometryCalib/fx_fy');
445            focal=[];%default fro old convention (Reg Wilson)
446            if isequal(length(uid_fx_fy),1)
447                tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value'));
448            else %old convention (Reg Wilson)
449                uid_focal=find(subt,'/GeometryCalib/focal');
450                uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy');
451                uid_sx=find(subt,'/GeometryCalib/sx');
452                if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx)
453                    dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value'));
454                    sx=str2num(get(subt,children(subt,uid_sx),'value'));
455                    focal=str2num(get(subt,children(subt,uid_focal),'value'));
456                    tsai.fx_fy(1)=sx*focal/dpx_dpy(1);
457                    tsai.fx_fy(2)=focal/dpx_dpy(2);
458                end
459            end
460            uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy');
461            if ~isempty(uid_Cx_Cy)
462                tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value'));
463            end
464            uid_kc=find(subt,'/GeometryCalib/kc');
465            if ~isempty(uid_kc)
466                tsai.kc=str2double(get(subt,children(subt,uid_kc),'value'));
467            else %old convention (Reg Wilson)
468                uid_kappa1=find(subt,'/GeometryCalib/kappa1');
469                if ~isempty(uid_kappa1)&& ~isempty(focal)
470                    kappa1=str2double(get(subt,children(subt,uid_kappa1),'value'));
471                    tsai.kc=-kappa1*focal*focal;
472                end
473            end
474            uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz');
475            if ~isempty(uid_Tx_Ty_Tz)
476                tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value'));
477            end
478            uid_R=find(subt,'/GeometryCalib/R');
479            if ~isempty(uid_R)
480                RR=get(subt,children(subt,uid_R),'value');
481                if length(RR)==3
482                    tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})];
483                end
484            end
485           
486            %look for laser plane definitions
487            uid_Angle=find(subt,'/GeometryCalib/PlaneAngle');
488            uid_Pos=find(subt,'/GeometryCalib/SliceCoord');
489            if isempty(uid_Pos)
490                uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention
491            end
492            if ~isempty(uid_Angle)
493                tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value'));
494            end
495            if ~isempty(uid_Pos)
496                for j=1:length(uid_Pos)
497                    tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value'));
498                end
499                uid_DZ=find(subt,'/GeometryCalib/SliceDZ');
500                uid_NbSlice=find(subt,'/GeometryCalib/NbSlice');
501                if ~isempty(uid_DZ) && ~isempty(uid_NbSlice)
502                    DZ=str2double(get(subt,children(subt,uid_DZ),'value'));
503                    NbSlice=get(subt,children(subt,uid_NbSlice),'value');
504                    if isequal(NbSlice,'volume')
505                        tsai.NbSlice='volume';
506                        NbSlice=NbDtj+1;
507                    else
508                        tsai.NbSlice=str2double(NbSlice);
509                    end
510                    tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1];
511                end
512            end   
513            tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]);
514            tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n');
515            tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]);
516            tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1);
517           
518            if strcmp(option,'GeometryCalib')
519                tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]);
520            end
521            s.GeometryCalib=tsai;
522        end
523    end
524end
525
526%--------------------------------------------------
527%  read a subtree
528% INPUT:
529% t: xltree
530% head_element: head elelemnt of the subtree
531% Data, structure containing
532%    .Key: element name
533%    .Type: type of element ('charg', 'float'....)
534%    .NbOccur: nbre of occurrence, NaN for un specified number
535function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
536%--------------------------------------------------
537s=[];%default
538errormsg='';
539head_element=get(subt,1,'name');
540    cont=get(subt,1,'contents');
541    if ~isempty(cont)
542        for ilist=1:length(Data)
543            uid_key=find(subt,[head_element '/' Data{ilist}]);
544            if ~isequal(length(uid_key),NbOccur(ilist))
545                errormsg=['wrong number of occurence for ' Data{ilist}];
546                return
547            end
548            for ival=1:length(uid_key)
549                val=get(subt,children(subt,uid_key(ival)),'value');
550                if ~NumTest(ilist)
551                    eval(['s.' Data{ilist} '=val;']);
552                else
553                    eval(['s.' Data{ilist} '=str2double(val);'])
554                end
555            end
556        end
557    end
558
559
560%--------------------------------------------------
561%  read an xml element
562function val=get_value(t,label,default)
563%--------------------------------------------------
564val=default;
565uid=find(t,label);%find the element iud(s)
566if ~isempty(uid) %if the element named label exists
567   uid_child=children(t,uid);%find the children
568   if ~isempty(uid_child)
569       data=get(t,uid_child,'type');%get the type of child
570       if iscell(data)% case of multiple element
571           for icell=1:numel(data)
572               val_read=str2num(get(t,uid_child(icell),'value'));
573               if ~isempty(val_read)
574                   val(icell,:)=val_read;
575               end
576           end
577%           val=val';
578       else % case of unique element value
579           val_read=str2num(get(t,uid_child,'value'));
580           if ~isempty(val_read)
581               val=val_read;
582           else
583              val=get(t,uid_child,'value');%char string data
584           end
585       end
586   end
587end
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