source: trunk/src/series/extract_rdvision.m @ 1051

Last change on this file since 1051 was 1051, checked in by sommeria, 5 years ago

psmsn cluster command updated, pb with multimask solved...

File size: 23.7 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 2008-2018, 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 ....
107    return
108end
109
110ParamOut=[];
111%%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
112%% read input parameters from an xml file if input is a file name (batch mode)
113
114if ischar(Param)
115    Param=xml2struct(Param);% read Param as input file (batch case)
116%     checkrun=0;
117end
118disp(Param)
119checkrun=strcmp(Param.RunMode,'local')
120hseries=findobj(allchild(0),'Tag','series');
121RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
122WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
123
124%% root input file(s) and type
125RootPath=Param.InputTable{1,1};
126if ~isempty(find(~strcmp(RootPath,Param.InputTable(:,1))))% if the Rootpath for each camera are not identical
127    disp_uvmat('ERROR','Rootpath for all cameras must be identical',checkrun)
128    return
129end
130
131% get the set of input file names (cell array filecell), and the lists of
132% input file or frame indices i1_series,i2_series,j1_series,j2_series
133[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
134
135%OutputDir=[Param.OutputSubDir Param.OutputDirExt];
136 
137% numbers of slices and file indices
138nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
139nbfield_i=size(i1_series{1},2); %nb of fields for the i index
140nbfield=nbfield_j*nbfield_i; %total number of fields
141
142%determine the file type on each line from the first input file
143
144FileInfo=get_file_info(filecell{1,1});
145if strcmp(FileInfo.FileType,'rdvision')
146    if ~isequal(FileInfo.NumberOfFrames,nbfield)
147        disp_uvmat('WARNING',['the whole series of ' num2str(FileInfo.NumberOfFrames) ' images must be extracted at once'],checkrun)
148        %rmfield(OutputDir)
149%         return
150    end
151    %% interactive input of specific parameters (for RDvision system)
152    display('converting images from RDvision system...')
153else
154    disp_uvmat('ERROR','the input is not from rdvision: a .seq or .sqb file must be opened',checkrun)
155    return
156end
157t=xmltree;
158
159save(t,fullfile(RootPath,'Running.xml'))%create an xml file to indicate that processing takes place
160
161%% calibration data and timing: read the ImaDoc files
162mode=''; %default
163timecell={};
164itime=0;
165NbSlice_calib={};
166
167%SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
168
169%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
170%%%  loop on the cameras ( #iview)
171%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
172% RootPath=Param.InputTable(:,1);
173% RootFile=Param.InputTable(:,3);
174% SubDir=Param.InputTable(:,2);
175% NomType=Param.InputTable(:,4);
176% FileExt=Param.InputTable(:,5);
177
178% [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
179% if size(time,1)>1
180%     diff_time=max(max(diff(time)));
181%     if diff_time>0
182%         disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
183%     end
184% end
185%
186%      nbfield2=size(time,1);
187checkpreserve=0;% if =1, will npreserve the original images, else it erases them at the end
188for iview=1:size(Param.InputTable,1)
189    for iview_xml=1:size(Param.InputTable,1)% look for the xml files in the different data directories
190        filexml=[fullfile(RootPath,Param.InputTable{iview_xml,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder
191        if exist(filexml,'file')
192            break
193        end
194    end
195    if ~exist(filexml,'file')
196        disp_uvmat('ERROR',[filexml ' missing'],checkrun)
197        return
198    end
199 
200    newxml=fullfile(RootPath,Param.InputTable{iview,3});
201    newxml=regexprep(newxml,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180'
202    newxml=[newxml '.xml'];
203   
204    %% get the names of .seq and .sqb files
205    switch Param.InputTable{iview,5}
206        case {'.seq','.sqb'}
207            filename_seq=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.seq']);
208            filename_sqb=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.sqb']);
209           
210            logdir=[Param.OutputSubDir Param.OutputDirExt];
211            [success,errormsg] = copyfile(filename_seq,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.seq']); %copy the seq file in the upper folder
212            [success,errormsg] = copyfile(filename_sqb,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.sqb']); %copy the sqb file in the upper folder
213            [success,errormsg] = copyfile(filexml,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.xml']); %copy the original xml file in the upper folder
214        otherwise
215            errormsg='input file extension must be .seq or .sqb';
216    end
217    if ~exist(filename_seq,'file')
218        errormsg=[filename_seq ' does not exist'];
219    end
220    if ~isempty(errormsg)
221        disp_uvmat('ERRROR',errormsg,checkrun);
222        return
223    end
224   
225
226    %% get data from .seq file
227    s=ini2struct(filename_seq);
228    SeqData=s.sequenceSettings;
229    SeqData.width=str2double(SeqData.width);
230    SeqData.height=str2double(SeqData.height);
231    SeqData.bytesperpixel=str2double(SeqData.bytesperpixel);
232    SeqData.nb_frames=str2double(s.sequenceSettings.numberoffiles);
233    if isempty(SeqData.binrepertoire)%used when binrepertoire empty, strange feature of rdvision
234        SeqData.binrepertoire=regexprep(s.sequenceSettings.bindirectory,'\\$','');%tranform Windows notation to Linux
235        SeqData.binrepertoire=regexprep(SeqData.binrepertoire,'\','/');
236        [tild,SeqData.binrepertoire,DirExt]=fileparts(SeqData.binrepertoire);
237    end
238   
239   
240   
241    %% reading the .sqb file
242    m = memmapfile(filename_sqb,'Format', { 'uint32' [1 1] 'offset'; ...
243        'uint32' [1 1] 'garbage1';...
244        'double' [1 1] 'timestamp';...
245        'uint32' [1 1] 'file_idx';...
246        'uint32' [1 1] 'garbage2' },'Repeat',SeqData.nb_frames);
247   
248    %%%%%%%BRICOLAGE in case of unreadable .sqb file: remplace lecture du fichier
249%             ind=[8356 8356:8672];%indices of bin files
250%             w=2432;%w=width of images in pixels
251%             h=864;%h=height of images in pixels
252%             bpp=2;% nbre of bytes per pixel
253%             lengthimage=w*h*bpp;% lengthof an image record on the binary file
254%             nbimages=15; %nbre of images of each camera in a bin file
255%             for ii=1:15*numel(ind)
256%                 %data(ii).offset=mod(ii-1,32)*2*lengthimage+lengthimage;%Dalsa_2
257%                 %data(ii).offset=mod(ii-1,32)*2*lengthimage;%Dalsa_1
258%                 %data(ii).file_idx=ind(ceil(ii/32));
259%                 data(ii).file_idx=ind(ceil(ii/15));
260%                 data(ii).timestamp=0.005*(ii-1);
261%             end
262%             m.Data=data;
263    %%%%%%%
264    timestamp=zeros(1,numel(m.Data));
265    for ii=1: numel(m.Data)
266        timestamp(ii)=m.Data(ii).timestamp;
267    end
268    [nbfield1,nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml); %copy the xml file in the upper folder
269    [XmlData,errormsg]=imadoc2struct(newxml);% check reading of the new xml file
270    if ~isempty(errormsg)
271        disp(errormsg)
272        return
273    end
274    timestamp=timestamp(1:nbfield1*nbfield2);
275    timestamp=reshape(timestamp,nbfield2,nbfield1);
276    difftime=XmlData.Time(2:end,2:end)'-timestamp;
277    disp(['time from xml and timestamp differ by ' num2str(max(max(abs(difftime))))])
278    if max(abs(difftime))>0.01
279        checkpreserve=1;% will not erase the initial files, possibility of error
280    end
281   
282        %% checking consistency with the xml file
283%     if ~isequal(SeqData.nb_frames,numel(timestamp))
284%         disp_uvmat('ERRROR',['inconsistent number of images ' num2str(SeqData.nb_frames) ' with respect to the xml file: ' num2str(numel(timestamp))] ,checkrun);
285%         return
286%     end   
287   
288    if nbfield2>1
289        NomTypeNew='_1_1';
290    else
291        NomTypeNew='_1';
292    end
293
294    [BinList,errormsg]=binread_rdv_series(RootPath,SeqData,m.Data,nbfield2,NomTypeNew);
295    if ~isempty(errormsg)
296        disp_uvmat('ERROR',errormsg,checkrun)
297        return
298    end
299   
300    % check the existence of the expected output image files (from the xml)
301    FileDir=SeqData.sequencename;
302     FileDir=regexprep(FileDir,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180'
303    for i1=1:numel(timestamp)/nbfield2
304        for j1=1:nbfield2
305            OutputFile=fullfile_uvmat(RootPath,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode
306            try
307            A=imread(OutputFile);% check image reading (stop if error)
308            catch ME
309                disp(['checking ' OutputFile])
310                disp(ME.message)
311            end
312        end
313    end
314end
315
316%% remove binary files if transfer OK
317%     if ~checkpreserve
318%         for iview=1:size(Param.InputTable,1)
319%          fullfile(RootPath,Param.InputTable{iview,2})
320%          source_dir=fullfile(RootPath,Param.InputTable{iview,2});
321%         [SUCCESS,MESSAGE]=rmdir(source_dir,'s')
322%         end
323%     end
324delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished
325
326%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
327%--------- reads a series of bin files
328
329%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
330function [BinList,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew)
331% BINREAD_RDV Permet de lire les fichiers bin g???n???r???s par Hiris ??? partir du
332% fichier seq associ???.
333%   [IMGS,TIMESTAMPS,NB_FRAMES] = BINREAD_RDV(FILENAME,FRAME_IDX) lit
334%   l'image d'indice FRAME_IDX de la s???quence FILENAME.
335%
336%   Entr???es
337%   -------
338%   FILENAME  : Nom du fichier s???quence (.seq).
339%   FRAME_IDX : Indice de l'image ??? lire. Si FRAME_IDX vaut -1 alors la
340%   s???quence est enti???rement lue. Si FRAME_IDX est un tableau d'indices
341%   alors toutes les images d'incides correspondant sont lues. Si FRAME_IDX
342%   est un tableau vide alors aucune image n'est lue mais le nombre
343%   d'images et tous les timestamps sont renvoy???s. Les indices commencent ???
344%   1 et se termines ??? NB_FRAMES.
345%
346%   Sorties
347%   -------
348%   IMGS        : Images de sortie.
349%   TIMESTAMPS  : Timestaps des images lues.
350%   NB_FRAMES   : Nombres d'images dans la s???quence.
351NbBinFile=0;
352BinSize=0;
353fid=0;
354errormsg='';
355BinList={};
356
357classname=sprintf('uint%d',SeqData.bytesperpixel*8);
358
359classname=['*' classname];
360BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits)
361%%%%
362% SeqData.binrepertoire='2017-01-26T11.59.57';
363%SeqData.binrepertoire='2017-01-26T16.57.27';
364%SeqData.binrepertoire='2017-01-26T19.28.05';
365%SeqData.binrepertoire='2017-01-27T09.51.34';
366%SeqData.binrepertoire='2017-01-27T14.21.47'
367%%%%
368binrepertoire=fullfile(PathDir,SeqData.binrepertoire);
369FileDir=SeqData.sequencename;
370FileDir=regexprep(FileDir,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180'
371OutputDir=fullfile(PathDir,FileDir);
372if ~exist(OutputDir,'dir')
373    %     errormsg=[OutputDir ' already exist, delete it first'];
374    %     return
375    % end
376    [s,errormsg]=mkdir(OutputDir);
377   
378    if s==0
379        disp(errormsg)
380        return%not able to create new image dir
381    end
382end
383bin_file_counter=0;
384for ii=1:SeqData.nb_frames
385    j1=[];
386    if ~isequal(nbfield2,1)
387        j1=mod(ii-1,nbfield2)+1;
388    end
389    i1=floor((ii-1)/nbfield2)+1;
390    OutputFile=fullfile_uvmat(PathDir,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode
391    fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx));
392    if exist(OutputFile,'file')% do not recreate existing image file
393        fid=0;
394    else
395        if fid==0 || ~strcmp(fname,fname_prev) % open the bin file if not in use
396            if fid~=0
397                fclose(fid);%close the previous bin file if relevant
398            end
399            [fid,msg]=fopen(fname,'rb');
400            if isequal(fid,-1)
401                errormsg=['error in opening ' fname ': ' msg];
402                return
403            else
404                disp([fname ' opened for reading'])
405                bin_file_counter=bin_file_counter+1;
406                BinList{bin_file_counter}=fname;
407            end
408            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
409            NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose)
410            BinSize(NbBinFile)=0;% strat counter for new bin file
411        else
412            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
413        end
414        fname_prev=fname;
415        A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image
416        A=A';
417        BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read
418        try
419            imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images
420            disp([OutputFile ' written']);
421            % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a')
422            %         if ~s
423            % %             disp_uvmat('ERROR',errormsg,checkrun);
424            %             return
425            %         end
426        catch ME
427            errormsg=ME.message;
428            return
429        end
430    end
431end
432if fid~=0
433fclose(fid)
434end
435
436
437
438
439function [nbfield1,nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml)
440msg='';
441t=xmltree(filexml);
442
443%% read Dtk and NbDtk
444NbDtk=1; %default
445Dtk=[]; % default
446uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk');
447uid_content_Dtk=get(t,uid_Dtk,'contents');
448if ~isempty(uid_content_Dtk)
449    Dtk=str2num(get(t,uid_content_Dtk,'value'));
450    uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
451    uid_content_NbDtk=get(t,uid_NbDtk,'contents');
452    if ~isempty(uid_content_NbDtk)
453    NbDtk=str2num(get(t,uid_content_NbDtk,'value'));
454    end
455end
456
457%% read Dti and NbDti
458NbDti=1; %default
459Dti=[]; % default
460uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti');
461uid_content_Dti=get(t,uid_Dti,'contents');
462if ~isempty(uid_content_Dti)
463    Dti=str2num(get(t,uid_content_Dti,'value'));
464    uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti');
465    uid_content_NbDti=get(t,uid_NbDti,'contents');
466    if ~isempty(uid_content_NbDti)
467    NbDti=str2num(get(t,uid_content_NbDti,'value'));
468    end
469end
470
471%% read Dtj and NbDtj
472NbDtj=1; %default
473Dtj=[]; % default
474uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj');
475uid_content_Dtj=get(t,uid_Dtj,'contents');
476if ~isempty(uid_content_Dtj)
477    Dtj=str2num(get(t,uid_content_Dtj,'value'));
478    uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
479    uid_content_NbDtj=get(t,uid_NbDtj,'contents');
480    if ~isempty(uid_content_NbDtj)
481    NbDtj=str2num(get(t,uid_content_NbDtj,'value'));
482    end
483end
484
485%% correct NbDtj and NbDti (error from RDvision)
486if NbDtj==numel(Dtj)% case of bursts
487    NbDtj=1;
488    uid_motor_nbslice=find(t,'ImaDoc/TranslationMotor/Nbslice');
489    if ~isempty(uid_motor_nbslice)&& ~isempty(uid_Dtk)% case of multilevel
490        NbSlice=str2num(get(t,get(t,uid_motor_nbslice,'contents'),'value'));
491        NbDti=NbSlice-1;
492    end
493end
494
495if isempty(Dtj)% case of simple series
496    timestamp=timestamp';
497    t=set(t,uid_content_NbDti,'value',num2str(numel(timestamp)-1));% correct NbDti in the xml file
498    nbfield1=numel(timestamp);
499    nbfield2=1;
500else
501    nbfieldi=(NbDti*numel(Dti)+1);
502    nbfieldk=(NbDtk*numel(Dtk)+1);
503    nbfield1=nbfieldi*nbfieldk;
504    nbfield2=NbDtj*numel(Dtj)+1;
505    NbFrames_xml=nbfield1*nbfield2;
506   if NbFrames_xml<numel(timestamp)
507       disp(['ERROR: size from xml ' num2str(NbFrame_xml) ' smaller than timestamp size ' num2str(numel(timestamp))])
508       return
509   end
510   if NbFrames_xml>numel(timestamp)
511       nbfield1=floor(numel(timestamp)/nbfield2);
512       nbfieldk=floor(nbfield1/nbfieldi);
513       nbfield1=nbfieldi*nbfieldk;
514       NbDtk=nbfieldk-1;
515       t=set(t,uid_content_NbDtk,'value',num2str(NbDtk));% correct NbDtk in the xml file (in practice numel(Dtk)=1;
516       timestamp=timestamp(1:nbfield1*nbfield2);
517       disp(['image record stopped before end: max index i= ' num2str(nbfield1)]);
518       timestamp=reshape(timestamp,nbfield2,nbfield1);
519   end
520   % check Dtj with respect to timestamp
521    timestamp=(reshape(timestamp,nbfield2,[]))';
522    diff_Dtj=diff(timestamp(1,:))-Dtj;
523    if max(abs(diff_Dtj))>min(Dtj)/1000
524        disp(['Dtj from xml file differs from time stamp by ' num2str(max(abs(diff_Dtj))) ', '])%'
525    else
526        disp('Dtj OK');
527    end
528end
529
530%% adjust Dti
531if NbDti+1>size(timestamp,1)
532    NbDti=size(timestamp,1)-1;
533end
534Dti_stamp=(timestamp(1+NbDti,1)-timestamp(1,1))/NbDti;
535t=set(t,uid_content_Dti,'value',num2str(Dti_stamp));%corret Dti
536if abs(Dti_stamp-Dti)>Dti/1000
537    disp([msg 'Dti from xml file corrected by ' num2str(Dti_stamp-Dti) ', ']);%'
538else
539    disp('Dti OK')
540end
541
542%% adjust Dtk
543if ~isempty(uid_Dtk)
544    Dtk_stamp=(timestamp((NbDti+1)*NbDtk+1,1)-timestamp(1,1))/NbDtk;
545    t=set(t,uid_content_Dtk,'value',num2str(Dtk_stamp));
546    if abs(Dtk_stamp-Dtk)>Dtk/1000
547        disp(['Dtk from xml file corrected by ' num2str(Dtk_stamp-Dtk)]);
548    else
549        disp('Dtk OK')
550    end
551    t=set(t,uid_content_Dtk,'value',num2str(Dtk_stamp));
552end
553
554%% save the new xml file
555save(t,newxml)
556[success,errormsg] = fileattrib(newxml,'+w','g');% allow writing access for the group of users
557if success==0
558    disp({['warning: unable to set group write access to ' newxml ':']; errormsg});%error message for directory creation
559    msg=errormsg;
560end
561
562
563
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