source: trunk/src/series/extract_rdvision.m @ 969

Last change on this file since 969 was 969, checked in by sommeria, 5 years ago

extract_rdvision updated

File size: 21.9 KB
Line 
1%'extract_rdvision': relabel an image series with two indices, and correct errors from the RDvision transfer program
2%------------------------------------------------------------------------
3% function ParamOut=extract_rdvision(Param)
4%------------------------------------------------------------------------
5%
6%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %
7%%%%%%%%%%%%%%%%%%%%%%%%%%
8%
9%OUTPUT
10% ParamOut: sets options in the GUI series.fig needed for the function
11%
12%INPUT:
13% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
14% In batch mode, Param is the name of the corresponding xml file containing the same information
15% when Param.Action.RUN=0 (as activated when the current Action is selected
16% in series), the function ouput paramOut set the activation of the needed GUI elements
17%
18% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
19% see the current structure Param)
20%    .InputTable: cell of input file names, (several lines for multiple input)
21%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
22%    .OutputSubDir: name of the subdirectory for data outputs
23%    .OutputDirExt: directory extension for data outputs
24%    .Action: .ActionName: name of the current activated function
25%             .ActionPath:   path of the current activated function
26%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
27%             .RUN =0 for GUI input, =1 for function activation
28%             .RunMode='local','background', 'cluster': type of function  use
29%             
30%    .IndexRange: set the file or frame indices on which the action must be performed
31%    .FieldTransform: .TransformName: name of the selected transform function
32%                     .TransformPath:   path  of the selected transform function
33%    .InputFields: sub structure describing the input fields withfields
34%              .FieldName: name(s) of the field
35%              .VelType: velocity type
36%              .FieldName_1: name of the second field in case of two input series
37%              .VelType_1: velocity type of the second field in case of two input series
38%              .Coord_y: name of y coordinate variable
39%              .Coord_x: name of x coordinate variable
40%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
41%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
42
43%=======================================================================
44% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
45%   http://www.legi.grenoble-inp.fr
46%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
47%
48%     This file is part of the toolbox UVMAT.
49%
50%     UVMAT is free software; you can redistribute it and/or modify
51%     it under the terms of the GNU General Public License as published
52%     by the Free Software Foundation; either version 2 of the license,
53%     or (at your option) any later version.
54%
55%     UVMAT is distributed in the hope that it will be useful,
56%     but WITHOUT ANY WARRANTY; without even the implied warranty of
57%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
58%     GNU General Public License (see LICENSE.txt) for more details.
59%=======================================================================
60
61function ParamOut=extract_rdvision(Param) %default output=relabel_i_j(Param)
62
63%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
64if isstruct(Param) && isequal(Param.Action.RUN,0)
65    ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
66    ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
67    ParamOut.NbSlice=1; ...%nbre of slices, 1 prevents splitting in several processes, ('off' by default)
68    ParamOut.VelType='off';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
69    ParamOut.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
70    ParamOut.FieldTransform = 'off';...%can use a transform function
71    ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on',
72    ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
73     ParamOut.OutputDirExt='.extract';%set the output dir extension
74    ParamOut.OutputSubDirMode='one'; %output folder given by the folder name of the first input line
75     % detect the set of image folder
76    RootPath=Param.InputTable{1,1};
77    ListStruct=dir(RootPath);   
78    ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
79    check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it
80    check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
81    ListDir=ListCells(1,find(check_dir & ~check_bad));
82%     InputTable=cell(numel(ListDir),5);
83%     InputTable(:,2)=ListDir';
84    isel=0;
85    InputTable=Param.InputTable;
86    for ilist=1:numel(ListDir)
87        ListStructSub=dir(fullfile(RootPath,ListDir{ilist}));
88        ListCellSub=struct2cell(ListStructSub);% transform dir struct to a cell arrray
89        detect_seq=regexp(ListCellSub(1,:),'.seq$');
90        seq_index=find(~cellfun('isempty',detect_seq),1);
91        if ~isempty(seq_index)
92%             msgbox_uvmat('ERROR',['not seq file in ' ListDir{ilist} ': please check the input folders'])
93%         else
94           isel=isel+1;
95           InputTable{isel,1}=RootPath;
96           InputTable{isel,2}=ListDir{ilist};
97            RootFile=regexprep(ListCellSub{1,seq_index},'.seq$','');
98            InputTable{isel,3}=RootFile;
99        InputTable{isel,4}='*';
100        InputTable{isel,5}='.seq';
101    end
102    end
103    hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
104    hhseries=guidata(hseries); %handles of the elements in 'series'
105    set(hhseries.InputTable,'Data',InputTable)
106    ParamOut.ActionInput.LogPath=RootPath;% indicate the path for the output info: 0_LOG ....
107return
108end
109
110ParamOut=[];
111%%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
112%% read input parameters from an xml file if input is a file name (batch mode)
113checkrun=1;
114if ischar(Param)
115    Param=xml2struct(Param);% read Param as input file (batch case)
116    checkrun=0;
117end
118hseries=findobj(allchild(0),'Tag','series');
119RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
120WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
121
122%% root input file(s) and type
123RootPath=Param.InputTable{1,1};
124if ~isempty(find(~strcmp(RootPath,Param.InputTable(:,1))))% if the Rootpath for each camera are not identical
125    disp_uvmat('ERROR','Rootpath for all cameras must be identical',checkrun)
126    return
127end
128
129% get the set of input file names (cell array filecell), and the lists of
130% input file or frame indices i1_series,i2_series,j1_series,j2_series
131[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
132
133%OutputDir=[Param.OutputSubDir Param.OutputDirExt];
134 
135% numbers of slices and file indices
136nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
137nbfield_i=size(i1_series{1},2); %nb of fields for the i index
138nbfield=nbfield_j*nbfield_i; %total number of fields
139
140%determine the file type on each line from the first input file
141
142FileInfo=get_file_info(filecell{1,1});
143if strcmp(FileInfo.FileType,'rdvision')
144    if ~isequal(FileInfo.NumberOfFrames,nbfield)
145        disp_uvmat('WARNING',['the whole series of ' num2str(FileInfo.NumberOfFrames) ' images must be extracted at once'],checkrun)
146        %rmfield(OutputDir)
147%         return
148    end
149    %% interactive input of specific parameters (for RDvision system)
150    display('converting images from RDvision system...')
151else
152    disp_uvmat('ERROR','the input is not from rdvision: a .seq or .sqb file must be opened',checkrun)
153    return
154end
155t=xmltree;
156
157save(t,fullfile(RootPath,'Running.xml'))%create an xml file to indicate that processing takes place
158
159%% calibration data and timing: read the ImaDoc files
160mode=''; %default
161timecell={};
162itime=0;
163NbSlice_calib={};
164
165%SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
166
167%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
168%%%  loop on the cameras ( #iview)
169%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
170% RootPath=Param.InputTable(:,1);
171% RootFile=Param.InputTable(:,3);
172% SubDir=Param.InputTable(:,2);
173% NomType=Param.InputTable(:,4);
174% FileExt=Param.InputTable(:,5);
175
176% [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
177% if size(time,1)>1
178%     diff_time=max(max(diff(time)));
179%     if diff_time>0
180%         disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
181%     end
182% end
183%
184%      nbfield2=size(time,1);
185checkpreserve=0;% if =1, will npreserve the original images, else it erases them at the end
186for iview=1:size(Param.InputTable,1)
187    for iview_xml=1:size(Param.InputTable,1)% look for the xml files in the different data directories
188        filexml=[fullfile(RootPath,Param.InputTable{iview_xml,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder
189        if exist(filexml,'file')
190            break
191        end
192    end
193    if ~exist(filexml,'file')
194        disp_uvmat('ERROR',[filexml ' missing'],checkrun)
195        return
196    end
197 
198    newxml=fullfile(RootPath,Param.InputTable{iview,3});
199    newxml=regexprep(newxml,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180'
200    newxml=[newxml '.xml'];
201   
202    %copyfile_modif(filexml,newxml); %copy the xml file in the upper folder
203   
204    %[XmlData,errormsg]=imadoc2struct(newxml);
205%     nbfield2=size(XmlData.Time,2)-1;
206%     if nbfield2>1
207%         NomTypeNew='_1_1';
208%     else
209%         NomTypeNew='_1';
210%     end
211    %% get the names of .seq and .sqb files
212    switch Param.InputTable{iview,5}
213        case {'.seq','.sqb'}
214            filename_seq=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.seq']);
215            filename_sqb=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.sqb']);
216            logdir=[Param.OutputSubDir Param.OutputDirExt];
217            [success,errormsg] = copyfile(filename_seq,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.seq']); %copy the seq file in the upper folder
218            [success,errormsg] = copyfile(filename_sqb,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.sqb']); %copy the sqb file in the upper folder
219        otherwise
220            errormsg='input file extension must be .seq or .sqb';
221    end
222    if ~exist(filename_seq,'file')
223        errormsg=[filename_seq ' does not exist'];
224    end
225    if ~isempty(errormsg)
226        disp_uvmat('ERRROR',errormsg,checkrun);
227        return
228    end
229   
230
231    %% get data from .seq file
232    s=ini2struct(filename_seq);
233    SeqData=s.sequenceSettings;
234    SeqData.width=str2double(SeqData.width);
235    SeqData.height=str2double(SeqData.height);
236    SeqData.bytesperpixel=str2double(SeqData.bytesperpixel);
237    SeqData.nb_frames=str2double(s.sequenceSettings.numberoffiles);
238    if isempty(SeqData.binrepertoire)%used when binrepertoire empty, strange feature of rdvision
239        SeqData.binrepertoire=regexprep(s.sequenceSettings.bindirectory,'\\$','');%tranform Windows notation to Linux
240        SeqData.binrepertoire=regexprep(SeqData.binrepertoire,'\','/');
241        [tild,binrepertoire,DirExt]=fileparts(SeqData.binrepertoire);
242        SeqData.binrepertoire=[SeqData.binrepertoire DirExt];
243    end
244   
245   
246   
247    %% reading the .sqb file
248    m = memmapfile(filename_sqb,'Format', { 'uint32' [1 1] 'offset'; ...
249        'uint32' [1 1] 'garbage1';...
250        'double' [1 1] 'timestamp';...
251        'uint32' [1 1] 'file_idx';...
252        'uint32' [1 1] 'garbage2' },'Repeat',SeqData.nb_frames);
253   
254    %%%%%%%BRICOLAGE in case of unreadable .sqb file: remplace lecture du fichier
255    %         ind=[111 114:211];%indices of bin files
256    %         w=1024;%w=width of images in pixels
257    %         h=1024;%h=height of images in pixels
258    %         bpp=2;% nbre of bytes per pixel
259    %         lengthimage=w*h*bpp;% lengthof an image record on the binary file
260    %         nbimages=32; %nbre of images of each camera in a bin file
261    %         for ii=1:32*numel(ind)
262    %             data(ii).offset=mod(ii-1,32)*2*lengthimage+lengthimage;%Dalsa_2
263    %             %data(ii).offset=mod(ii-1,32)*2*lengthimage;%Dalsa_1
264    %             data(ii).file_idx=ind(ceil(ii/32));
265    %             data(ii).timestamp=0.2*(ii-1);
266    %         end
267    %         m.Data=data;
268    %%%%%%%
269    timestamp=zeros(1,numel(m.Data));
270    for ii=1: numel(m.Data)
271        timestamp(ii)=m.Data(ii).timestamp;
272%         j1=1;
273%         if ~isequal(nbfield2,1)
274%             j1=mod(ii-1,nbfield2)+1;
275%         end
276%         i1=floor((ii-1)/nbfield2)+1;
277        %diff_time(i1,j1)= timestamp(ii)-XmlData.Time(i1+1,j1+1);
278    end
279    [nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml); %copy the xml file in the upper folder
280    [XmlData,errormsg]=imadoc2struct(newxml);% check reading of the new xml file
281    if ~isempty(errormsg)
282        disp(errormsg)
283        return
284    end
285    difftime=XmlData.Time(2:end,2:end)-(reshape(timestamp,nbfield2,[]))';
286    disp(['time from xml and timestamp differ by ' num2str(max(max(abs(difftime))))])
287    if max(abs(difftime))>0.01
288        checkpreserve=1;% will not erase the initial files, possibility of error
289    end
290   
291        %% checking consistency with the xml file
292    if ~isequal(SeqData.nb_frames,numel(timestamp))
293        disp_uvmat('ERRROR',['inconsistent number of images ' num2str(SeqData.nb_frames) ' with respect to the xml file: ' num2str(numel(timestamp))] ,checkrun);
294        return
295    end   
296   
297    if nbfield2>1
298        NomTypeNew='_1_1';
299    else
300        NomTypeNew='_1';
301    end
302
303    [BinList,errormsg]=binread_rdv_series(RootPath,SeqData,m.Data,nbfield2,NomTypeNew);
304    if ~isempty(errormsg)
305        disp_uvmat('ERROR',errormsg,checkrun)
306        return
307    end
308   
309    % check the existence of the expected output image files (from the xml)
310    FileDir=SeqData.sequencename;
311     FileDir=regexprep(FileDir,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180'
312    for i1=1:numel(timestamp)/nbfield2
313        for j1=1:nbfield2
314            OutputFile=fullfile_uvmat(RootPath,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode
315            try
316            A=imread(OutputFile);% check image reading (stop if error)
317            catch ME
318                disp(['checking ' OutputFile])
319                disp(ME.message)
320            end
321        end
322    end
323end
324
325%% remove binary files if transfer OK
326    if ~checkpreserve
327        for iview=1:size(Param.InputTable,1)
328         fullfile(RootPath,Param.InputTable{iview,2})
329
330        [SUCCESS,MESSAGE]=rmdir(fullfile(RootPath,Param.InputTable{iview,2}),'s')
331        end
332    end
333delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished
334
335%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
336%--------- reads a series of bin files
337
338%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
339function [BinList,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew)
340% BINREAD_RDV Permet de lire les fichiers bin g???n???r???s par Hiris ??? partir du
341% fichier seq associ???.
342%   [IMGS,TIMESTAMPS,NB_FRAMES] = BINREAD_RDV(FILENAME,FRAME_IDX) lit
343%   l'image d'indice FRAME_IDX de la s???quence FILENAME.
344%
345%   Entr???es
346%   -------
347%   FILENAME  : Nom du fichier s???quence (.seq).
348%   FRAME_IDX : Indice de l'image ??? lire. Si FRAME_IDX vaut -1 alors la
349%   s???quence est enti???rement lue. Si FRAME_IDX est un tableau d'indices
350%   alors toutes les images d'incides correspondant sont lues. Si FRAME_IDX
351%   est un tableau vide alors aucune image n'est lue mais le nombre
352%   d'images et tous les timestamps sont renvoy???s. Les indices commencent ???
353%   1 et se termines ??? NB_FRAMES.
354%
355%   Sorties
356%   -------
357%   IMGS        : Images de sortie.
358%   TIMESTAMPS  : Timestaps des images lues.
359%   NB_FRAMES   : Nombres d'images dans la s???quence.
360NbBinFile=0;
361BinSize=0;
362fid=0;
363errormsg='';
364BinList={};
365
366classname=sprintf('uint%d',SeqData.bytesperpixel*8);
367
368classname=['*' classname];
369BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits)
370binrepertoire=fullfile(PathDir,SeqData.binrepertoire);
371FileDir=SeqData.sequencename;
372FileDir=regexprep(FileDir,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180'
373OutputDir=fullfile(PathDir,FileDir);
374if ~exist(OutputDir,'dir')
375    %     errormsg=[OutputDir ' already exist, delete it first'];
376    %     return
377    % end
378    [s,errormsg]=mkdir(OutputDir);
379   
380    if s==0
381        disp(errormsg)
382        return%not able to create new image dir
383    end
384end
385bin_file_counter=0;
386for ii=1:SeqData.nb_frames
387    j1=[];
388    if ~isequal(nbfield2,1)
389        j1=mod(ii-1,nbfield2)+1;
390    end
391    i1=floor((ii-1)/nbfield2)+1;
392    OutputFile=fullfile_uvmat(PathDir,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode
393    fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx));
394    if exist(OutputFile,'file')% do not recreate existing image file
395        fid=0;
396    else
397        if fid==0 || ~strcmp(fname,fname_prev) % open the bin file if not in use
398            if fid~=0
399                fclose(fid);%close the previous bin file if relevant
400            end
401            [fid,msg]=fopen(fname,'rb');
402            if isequal(fid,-1)
403                errormsg=['error in opening ' fname ': ' msg];
404                return
405            else
406                disp([fname ' opened for reading'])
407                bin_file_counter=bin_file_counter+1;
408                BinList{bin_file_counter}=fname;
409            end
410            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
411            NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose)
412            BinSize(NbBinFile)=0;% strat counter for new bin file
413        else
414            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
415        end
416        fname_prev=fname;
417        A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image
418        A=A';
419        BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read
420        try
421            imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images
422            disp([OutputFile ' written']);
423            % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a')
424            %         if ~s
425            % %             disp_uvmat('ERROR',errormsg,checkrun);
426            %             return
427            %         end
428        catch ME
429            errormsg=ME.message;
430            return
431        end
432    end
433end
434if fid~=0
435fclose(fid)
436end
437
438
439
440
441function [nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml)
442msg='';
443t=xmltree(filexml);
444
445%% correct NbDtj
446uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
447uid_content=get(t,uid_NbDtj,'contents');
448t=set(t,uid_content,'value','1');% set NbDtj to 1 (correct error in the xml file)
449
450%% check Dtj
451uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj');
452uid_content=get(t,uid_Dtj,'contents');
453Dtjstring=get(t,uid_content,'value');
454if isempty(Dtjstring)
455    timestamp=timestamp';
456    nbfield2=1;
457else
458    Dtj=str2num(get(t,uid_content,'value'));
459    nbfield2=numel(Dtj)+1;
460    timestamp=(reshape(timestamp,nbfield2,[]))';
461    diff_Dtj=diff(timestamp(1,:))-Dtj;
462    if max(abs(diff_Dtj))>min(Dtj)/1000
463        disp(['Dtj from xml file differs from time stamp by ' num2str(max(abs(diff_Dtj))) ', '])%'
464    else
465        disp('Dtj OK');
466    end
467end
468%% correct NbDti
469NbDti=size(timestamp,1)-1; %default for series or burst
470uid_motor_nbslice=find(t,'ImaDoc/TranslationMotor/Nbslice');
471uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
472if ~isempty(uid_motor_nbslice)&& ~isempty(uid_NbDtk)
473    uid_content=get(t,uid_motor_nbslice,'contents');
474    NbSlice=str2num(get(t,uid_content,'value'));
475    NbDti=NbSlice-1;
476    uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti');
477    uid_content=get(t,uid_NbDti,'contents');
478    t=set(t,uid_content,'value',num2str(NbDti));
479end
480
481%% adjust Dti
482uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti');
483uid_content=get(t,uid_Dti,'contents');
484Dti=str2num(get(t,uid_content,'value'));
485Dti_stamp=(timestamp(1+NbDti,1)-timestamp(1,1))/NbDti;
486if abs(Dti_stamp-Dti)>Dti/1000
487    disp([msg 'Dti from xml file corrected by ' num2str(Dti_stamp-Dti) ', ']);%'
488else
489    disp('Dti OK')
490end
491t=set(t,uid_content,'value',num2str(Dti_stamp));
492
493%% adjust Dtk
494uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk');
495if ~isempty(uid_Dtk)
496    uid_content_Dtk=get(t,uid_Dtk,'contents');
497    Dtk=str2num(get(t,uid_content_Dtk,'value'));
498    uid_content_NbDtk=get(t,uid_NbDtk,'contents');
499    NbDtk=str2num(get(t,uid_content_NbDtk,'value'));
500    Dtk_stamp=(timestamp(end-NbDti,1)-timestamp(1,1))/NbDtk;
501    if abs(Dtk_stamp-Dtk)>Dtk/1000
502        disp(['Dtk from xml file corrected by ' num2str(Dtk_stamp-Dtk)]);
503    else
504        disp('Dtk OK')
505    end
506    t=set(t,uid_content_Dtk,'value',num2str(Dtk_stamp));
507end
508
509save(t,newxml)
510[success,errormsg] = fileattrib(newxml,'+w','g');% allow writing access for the group of users
511if success==0
512    disp({['warning: unable to set group write access to ' newxml ':']; errormsg});%error message for directory creation
513    msg=errormsg;
514end
515
516
517
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