source: trunk/src/series/extract_rdvision.m

%'extract_rdvision': relabel an image series with two indices, and correct errors from the RDvision transfer program
%------------------------------------------------------------------------
% function ParamOut=extract_rdvision(Param)
%------------------------------------------------------------------------
%
%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %
%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%OUTPUT
% ParamOut: sets options in the GUI series.fig needed for the function
%
%INPUT:
% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
% In batch mode, Param is the name of the corresponding xml file containing the same information
% when Param.Action.RUN=0 (as activated when the current Action is selected
% in series), the function ouput paramOut set the activation of the needed GUI elements
%
% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
% see the current structure Param)
%    .InputTable: cell of input file names, (several lines for multiple input)
%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
%    .OutputSubDir: name of the subdirectory for data outputs
%    .OutputDirExt: directory extension for data outputs
%    .Action: .ActionName: name of the current activated function
%             .ActionPath:   path of the current activated function
%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
%             .RUN =0 for GUI input, =1 for function activation
%             .RunMode='local','background', 'cluster': type of function  extract_rdvision.muse
%
%    .IndexRange: set the file or frame indices on which the action must be performed
%    .FieldTransform: .TransformName: name of the selected transform function
%                     .TransformPath:   path  of the selected transform function
%    .InputFields: sub structure describing the input fields withfields
%              .FieldName: name(s) of the field
%              .VelType: velocity type
%              .FieldName_1: name of the second field in case of two input series
%              .VelType_1: velocity type of the second field in case of two input series
%              .Coord_y: name of y coordinate variable
%              .Coord_x: name of x coordinate variable
%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%=======================================================================
% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
%   http://www.legi.grenoble-inp.fr
%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
%
%     This file is part of the toolbox UVMAT.
%
%     UVMAT is free software; you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published
%     by the Free Software Foundation; either version 2 of the license,
%     or (at your option) any later version.
%
%     UVMAT is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License (see LICENSE.txt) for more details.extract_rdvision.m
%=======================================================================

function ParamOut=extract_rdvision(Param) %default output=relabel_i_j(Param)

%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
if isstruct(Param) && isequal(Param.Action.RUN,0)
    ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
        ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
        ParamOut.NbSlice='off';%1; ...%nbre of slices, 1 prevents splitting in several processes, ('off' by default)
    ParamOut.VelType='off';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
        ParamOut.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
        ParamOut.FieldTransform = 'off';...%can use a transform function
        ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on',
        ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
         ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
        ParamOut.CPUTime=0.25;% expected time for writting one image ( in minute)
    ParamOut.OutputDirExt='.extract';%set the output dir extension
    ParamOut.OutputSubDirMode='one'; %output folder given by the folder name of the first input line
    % detect the set of image folder
    RootPath=Param.InputTable{1,1};
    ListStruct=dir(RootPath);
    ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
    check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it
    check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
    ListDir=ListCells(1,find(check_dir & ~check_bad));
    isel=0;
    InputTable=Param.InputTable;
    for ilist=1:numel(ListDir)
        ListStructSub=dir(fullfile(RootPath,ListDir{ilist}));
        ListCellSub=struct2cell(ListStructSub);% transform dir struct to a cell arrray
        detect_seq=regexp(ListCellSub(1,:),'.seq$');
        seq_index=find(~cellfun('isempty',detect_seq),1);
        if ~isempty(seq_index)
            isel=isel+1;
            InputTable{isel,1}=RootPath;
            InputTable{isel,2}=ListDir{ilist};
            RootFile=regexprep(ListCellSub{1,seq_index},'.seq$','');
            InputTable{isel,3}=RootFile;
            InputTable{isel,4}='*';
            InputTable{isel,5}='.seq';
        end
    end
    hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
    hhseries=guidata(hseries); %handles of the elements in 'series'
    set(hhseries.InputTable,'Data',InputTable)
    ParamOut.ActionInput.LogPath=RootPath;% indicate the path for the output info: 0_LOG ....

    % check the names of .seq and .sqb files
    iview=1;
    if ~ismember(Param.InputTable{iview,5},{'.seq','.sqb'})
        msgbox_uvmat('ERROR','bad input file : select .seq or .sqb for image extraction');
        return
    end
    filename_seq=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.seq']);
    filename_sqb=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.sqb']);
    if ~exist(filename_seq,'file')
        msgbox_uvmat('ERROR',[filename_seq ' missing']);
        return
    end
    if ~exist(filename_sqb,'file')
        msgbox_uvmat('ERROR',[filename_sqb ' missing']);
        return
    end
    filexml=[fullfile(RootPath,Param.InputTable{iview,2},Param.InputTable{iview,3}) '.xml'];%xml at the level of the image folder
    if exist(filexml,'file')
        [XmlData,errormsg]=imadoc2struct(filexml);
        if isempty(errormsg)
            msgbox_uvmat('CONFIRMATION',[filexml ' used' ]);
        else
            msgbox_uvmat('ERROR',errormsg);
            return
        end
        ParamOut.ActionInput.Createxml=false;
        %  filexml=uigetfile_uvmat('pick xml file for timing',fullfile(RootPath,Param.InputTable{iview,2}),'.xml');
        % msgbox_uvmat('ERROR',[filexml ' missing: needed to get the image organisation and timing ']);
    else
        if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'BurstLength')
            BurstLength=num2str(Param.ActionInput.BurstLength);
        else
            BurstLength='1';%default for a simple image series
        end
         answer=msgbox_uvmat('INPUT_TXT',{['no xml file in ' Param.InputTable{iview,2}];' introduce the nbre of frames in a burst to create xml'},BurstLength);
        ParamOut.ActionInput.BurstLength=str2double(answer);
         % filexml=uigetfile_uvmat('pick xml file for timing',fullfile(RootPath,Param.InputTable{iview,2}),'.xml');
        % [XmlData,errormsg]=imadoc2struct(filexml);
        ParamOut.ActionInput.Createxml=true;
    end

% get data from .seq file
    s=ini2struct(filename_seq);
    SeqData=s.sequenceSettings;
    SeqData.nb_frames=str2double(s.sequenceSettings.numberoffiles);
% reading the .sqb file
    m = memmapfile(filename_sqb,'Format', { 'uint32' [1 1] 'offset'; ...
        'uint32' [1 1] 'garbage1';...
        'double' [1 1] 'timestamp';...
        'uint32' [1 1] 'file_idx';...
        'uint32' [1 1] 'garbage2' },'Repeat',SeqData.nb_frames);
    ParamOut.ActionInput.XmlData.SourceFolder=fileparts(m.Filename);
        timestamp=zeros(1,numel(m.Data));
        for ii=1: numel(m.Data)
            timestamp(ii)=m.Data(ii).timestamp;
        end
        
%         
%         %%%%%BRICOLAGE EXP40
%         ind1=5*59-10;
%         ind2=12*59-10;
%         ind3=119*59-10;
%         ind4=483*59-10;
%         timestamp=[timestamp(1:ind4) timestamp(ind4) timestamp(ind4+1:end)];
%          timestamp=[timestamp(1:ind3) timestamp(ind3) timestamp(ind3+1:end)];
%           timestamp=[timestamp(1:ind2) timestamp(ind2) timestamp(ind2+1:end)];
%            timestamp=[timestamp(1:ind1) timestamp(ind1) timestamp(ind1+1:end)];
%            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
           
           
        if ParamOut.ActionInput.Createxml
            ParamOut.ActionInput.XmlData.Camera.BurstTiming=time2xmlburst(timestamp,ParamOut.ActionInput.BurstLength);
            Time=xmlburst2time(ParamOut.ActionInput.XmlData.Camera.BurstTiming);
        else
           Time=XmlData.Time;
        end
        timexml=reshape(Time(2:end,2:end)',1,[]);
        if numel(timestamp)<= numel(timexml)
            timexml=timexml(1:numel(timestamp));
        else 
            msgbox_uvmat('ERROR',['time sequence from the xml file = ' num2str(numel(timexml))  ' smaller than timestamp length ' num2str(numel(timestamp))])
            return
        end
        difftime=timestamp-timexml;
        %if max(difftime)>0.01

        figure
        plot(timestamp,difftime)
        xlabel('timestamps(s)')
        ylabel('time difference(s)')
        title('discrepency timestamps-timexml') 
        %end
    return
end


%%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
ParamOut=[];
%% read input parameters from an xml file if input is a file name (batch mode)

if ischar(Param)
    Param=xml2struct(Param);% read Param as input file (batch case)
end
disp(Param)
checkrun=strcmp(Param.RunMode,'local');
hseries=findobj(allchild(0),'Tag','series');
RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series

%% root input file(s) and type
RootPath=Param.InputTable{1,1};
if ~isempty(find(~strcmp(RootPath,Param.InputTable(:,1))))% if the Rootpath for each camera are not identical
    disp_uvmat('ERROR','Rootpath for all cameras must be identical',checkrun)
    return
end

% get the set of input file names (cell array filecell), and the lists of
% input file or frame indices i1_series,i2_series,j1_series,j2_series
[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
 
% numbers of slices and file indices
nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
nbfield_i=size(i1_series{1},2); %nb of fields for the i index
nbfield=nbfield_j*nbfield_i; %total number of fields

%determine the file type on each line from the first input file 
FileInfo=get_file_info(filecell{1,1});
if strcmp(FileInfo.FileType,'rdvision')

    %% interactive input of specific parameters (for RDvision system)
    display('converting images from RDvision system...')
else
    disp_uvmat('ERROR','the input is not from rdvision: a .seq or .sqb file must be opened',checkrun)
    return
end
t=xmltree;

save(t,fullfile(RootPath,'Running.xml'))%create an xml file to indicate that processing takes place

%% calibration data and timing: read the ImaDoc files
mode=''; %default
timecell={};
itime=0;
NbSlice_calib={};

%SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  loop on the cameras ( #iview)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

for iview=1:size(Param.InputTable,1)
    check_xml=0;
    for iview_xml=1:size(Param.InputTable,1)% look for the xml files in the different data directories
        filexml=[fullfile(RootPath,Param.InputTable{iview_xml,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder
        if exist(filexml,'file')
            check_xml=1;
            break
        end
    end
    newxml=fullfile(RootPath,Param.InputTable{iview,3});
    newxml=regexprep(newxml,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180'extract_rdvision.m
    newxml=[newxml '.xml'];
    
    %% get the names of .seq and .sqb files and save them to the log output folder .extract
    if ismember( Param.InputTable{iview,5}, {'.seq','.sqb'})
            filename_seq=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.seq']);
            filename_sqb=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.sqb']);
            errormsg='';
            % backup of the seq, sqb and xml files for the first frame index
            if isequal(Param.IndexRange.first_i,1)% backup of the seq, sqb and xml files for the first frame index
                logdir=[Param.OutputSubDir Param.OutputDirExt];
                [success,errormsg] = copyfile(filename_seq,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.seq']); %copy the seq file in the upper folder
                if ~success
                    disp(errormsg)
                end
                [success,errormsg] = copyfile(filename_sqb,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.sqb']); %copy the sqb file in the upper folder
                if ~success
                    disp(errormsg)
                end
                if check_xml
                    [success,errormsg] = copyfile(filexml,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.xml']); %copy the original xml file in the upper folder
                    if ~success
                        disp(errormsg)
                    end
                end
            end
    else
            errormsg='input file extension must be .seq or .sqb';
    end
    if ~exist(filename_seq,'file')
        errormsg=[filename_seq ' does not exist'];
    end
    if ~isempty(errormsg)
        disp_uvmat('ERRROR',errormsg,checkrun);
        return
    end
   

    %% get data from .seq file
    s=ini2struct(filename_seq);
    SeqData=s.sequenceSettings;
    SeqData.width=str2double(SeqData.width);
    SeqData.height=str2double(SeqData.height);
    SeqData.bytesperpixel=str2double(SeqData.bytesperpixel);
    SeqData.nb_frames=str2double(s.sequenceSettings.numberoffiles);
    if isempty(SeqData.binrepertoire)%used when binrepertoire empty, strange feature of rdvision
        SeqData.binrepertoire=regexprep(s.sequenceSettings.bindirectory,'\\$','');%tranform Windows notation to Linux
        SeqData.binrepertoire=regexprep(SeqData.binrepertoire,'\','/');
        [tild,SeqData.binrepertoire,DirExt]=fileparts(SeqData.binrepertoire);
    end
    
    %% reading the .sqb file
    m = memmapfile(filename_sqb,'Format', { 'uint32' [1 1] 'offset'; ...
        'uint32' [1 1] 'garbage1';...
        'double' [1 1] 'timestamp';...
        'uint32' [1 1] 'file_idx';...
        'uint32' [1 1] 'garbage2' },'Repeat',SeqData.nb_frames);
    
    %%%%%%%BRICOLAGE in case of unreadable .sqb file: remplace lecture du fichier
%             ind=[8356 8356:8672];%indices of bin files
%             w=2432;%w=width of images in pixels
%             h=864;%h=height of images in pixels
%             bpp=2;% nbre of bytes per pixel
%             lengthimage=w*h*bpp;% lengthof an image record on the binary file
%             nbimages=15; %nbre of images of each camera in a bin file
%             for ii=1:15*numel(ind)
%                 %data(ii).offset=mod(ii-1,32)*2*lengthimage+lengthimage;%Dalsa_2
%                 %data(ii).offset=mod(ii-1,32)*2*lengthimage;%Dalsa_1
%                 %data(ii).file_idx=ind(ceil(ii/32));
%                 data(ii).file_idx=ind(ceil(ii/15));
%                 data(ii).timestamp=0.005*(ii-1);
%             end
%             m.Data=data;
%%%%%%%
if Param.ActionInput.Createxml
    nbfield2=Param.ActionInput.BurstLength;
else
    [XmlData,errormsg]=imadoc2struct(filexml);% check reading of the xml file
    if isempty(errormsg)
        nbfield2=size(XmlData.Time,2)-1;
    else
        disp(errormsg)
        return
    end
end



% timestamp=zeros(1,numel(m.Data));
% for ii=1: numel(m.Data)
%     timestamp(ii)=m.Data(ii).timestamp;
% end
if isequal(Param.IndexRange.first_i,1)
    if Param.ActionInput.Createxml
        t=struct2xml(Param.ActionInput.XmlData);
        t=set(t,1,'name','ImaDoc');
        save(t,newxml)
    else
        [success,errormsg]=copyfile(filexml,newxml);
    end
    % [nbfield1,nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml); %copy the xml file in the upper folder
    % if numel(timestamp)~=nbfield1*nbfield2
    %     disp('WARNING: total image number defined by the xml file differs from  the number of frames ')
    % else
    %     timestamp=reshape(timestamp,nbfield2,nbfield1);
    %     difftime=XmlData.Time(2:end,2:end)'-timestamp;
    %     disp(['time from xml and timestamp differ by ' num2str(max(max(abs(difftime))))])
    %     if max(abs(difftime))>0.01
    %         checkpreserve=1;% will not erase the initial files, possibility of error
    %     end
    % end
end
if nbfield2>1
    NomTypeNew='_1_1';
else
    NomTypeNew='_1';
end

[BinList,errormsg]=binread_rdv_series(RootPath,SeqData,m.Data,nbfield2,NomTypeNew,Param.IndexRange.first_i,Param.IndexRange.last_i,Param.CheckOverwrite);
if ~isempty(errormsg)
    disp_uvmat('ERROR',errormsg,checkrun)
    return
end
end
%% remove binary files if transfer OK
%     if ~checkpreserve
%         for iview=1:size(Param.InputTable,1)
%          fullfile(RootPath,Param.InputTable{iview,2})
%          source_dir=fullfile(RootPath,Param.InputTable{iview,2});
%         [SUCCESS,MESSAGE]=rmdir(source_dir,'s')
%         end
%     end
delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%--------- reads a series of bin files

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [BinList,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew,first,last,checkoverwrite)
% BINREAD_RDV Permet de lire les fichiers bin g???n???r???s par Hiris ??? partir du
% fichier seq associ???.
%   [IMGS,TIMESTAMPS,NB_FRAMES] = BINREAD_RDV(FILENAME,FRAME_IDX) lit
%   l'image d'indice FRAME_IDX de la s???quence FILENAME.
%
%   Entr???es
%   -------
%   FILENAME  : Nom du fichier s???quence (.seq).
%   FRAME_IDX : Indice de l'image ??? lire. Si FRAME_IDX vaut -1 alors la
%   s???quence est enti???rement lue. Si FRAME_IDX est un tableau d'indices
%   alors toutes les images d'incides correspondant sont lues. Si FRAME_IDX
%   est un tableau vide alors aucune image n'est lue mais le nombre
%   d'images et tous les timestamps sont renvoy???s. Les indices commencent ???
%   1 et se termines ??? NB_FRAMES.
%
%   Sorties
%   -------
%   IMGS        : Images de sortie.
%   TIMESTAMPS  : Timestaps des images lues.
%   NB_FRAMES   : Nombres d'images dans la s???quence.
NbBinFile=0;
BinSize=0;
fid=0;
errormsg='';
BinList={};

classname=sprintf('uint%d',SeqData.bytesperpixel*8);

classname=['*' classname];
BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits)
%%%%
% SeqData.binrepertoire='2017-01-26T11.59.57';
%SeqData.binrepertoire='2017-01-26T16.57.27';
%SeqData.binrepertoire='2017-01-26T19.28.05';
%SeqData.binrepertoire='2017-01-27T09.51.34';
%SeqData.binrepertoire='2017-01-27T14.21.47'
%%%%
binrepertoire=fullfile(PathDir,SeqData.binrepertoire);
FileDir=SeqData.sequencename;
FileDir=regexprep(FileDir,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180'
OutputDir=fullfile(PathDir,FileDir);
if ~exist(OutputDir,'dir')
    %     errormsg=[OutputDir ' already exist, delete it first'];
    %     return
    % end
    [s,errormsg]=mkdir(OutputDir);
    
    if s==0
        disp(errormsg)
        return%not able to create new image dir
    end
end
bin_file_counter=0;
%for ii=1:SeqData.nb_frames
 %%%%%BRICOLAGE EXP40
        ind1=5*59-10;
        ind2=12*59-10;
        ind3=119*59-10;
        ind4=483*59-10;

for ii=first:last
    j1=[];
    iinew=ii; 
%     %%%%%BRICOLAGE EXP40
%     switch ii
%         case  ii>=ind1 && ii<ind2
%       iinew=ii+1;
%         case ii>=ind2 && ii<ind3
%         iinew=ii+2;
%         case  ii>=ind3 && ii<ind4
%       iinew=ii+3;
%         case       ii>=ind4 && ii<ind3
%         iinew=ii+4;    
%     end
%      %%%%%%%%%
    if ~isequal(nbfield2,1)
        j1=mod(iinew-1,nbfield2)+1;
    end
    i1=floor((iinew-1)/nbfield2)+1;
    
    OutputFile=fullfile_uvmat(PathDir,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode
    fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx));
    if  ~checkoverwrite && exist(OutputFile,'file') % manage the overwrite of existing files (default=1) % manage the overwrite of existing files (default=1)exist(OutputFile,'file')% do not recreate existing image file
        fid=0;
    else
        if fid==0 || ~strcmp(fname,fname_prev) % open the bin file if not in use
            if fid~=0
                fclose(fid);%close the previous bin file if relevant
            end
            [fid,msg]=fopen(fname,'rb');
            if isequal(fid,-1)
                errormsg=['error in opening ' fname ': ' msg];
                return
            else
                disp([fname ' opened for reading'])
                bin_file_counter=bin_file_counter+1;
                BinList{bin_file_counter}=fname;
            end
            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
            NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose)
            BinSize(NbBinFile)=0;% strat counter for new bin file
        else
            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
        end
        fname_prev=fname;
        A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image
        A=A';
        BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read
        try
            tic
            imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images
            disp([OutputFile ' written']);
            toc
            % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a')
            %         if ~s
            % %             disp_uvmat('ERROR',errormsg,checkrun);
            %             return
            %         end
        catch ME
            errormsg=ME.message;
            return
        end
    end
end
if fid~=0
fclose(fid)
end
disp('END EXTRACT')


%OBSOLETE
function [nbfield1,nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml)%
msg='';
t=xmltree(filexml);

%% read Dtk and NbDtk
NbDtk=1; %default
Dtk=[]; % default
uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk');
uid_content_Dtk=get(t,uid_Dtk,'contents');
if ~isempty(uid_content_Dtk) 
    Dtk=str2num(get(t,uid_content_Dtk,'value'));
    uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
    uid_content_NbDtk=get(t,uid_NbDtk,'contents');
    if ~isempty(uid_content_NbDtk)
    NbDtk=str2num(get(t,uid_content_NbDtk,'value'));
    end
end

%% read Dti and NbDti
NbDti=1; %default
Dti=[]; % default
uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti');
uid_content_Dti=get(t,uid_Dti,'contents');
if ~isempty(uid_content_Dti) 
    Dti=str2num(get(t,uid_content_Dti,'value'));
    uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti');
    uid_content_NbDti=get(t,uid_NbDti,'contents');
    if ~isempty(uid_content_NbDti)
    NbDti=str2num(get(t,uid_content_NbDti,'value'));
    end
end

%% read Dtj and NbDtj
NbDtj=1; %default
Dtj=[]; % default
uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj');
uid_content_Dtj=get(t,uid_Dtj,'contents');
if ~isempty(uid_content_Dtj) 
    Dtj=str2num(get(t,uid_content_Dtj,'value'));
    uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
    uid_content_NbDtj=get(t,uid_NbDtj,'contents');
    if ~isempty(uid_content_NbDtj)
    NbDtj=str2num(get(t,uid_content_NbDtj,'value'));
    end
end

%% correct NbDtj and NbDti (error from RDvision)
% if NbDtj==numel(Dtj)% case of bursts
%     NbDtj=1;
%     uid_motor_nbslice=find(t,'ImaDoc/TranslationMotor/Nbslice');
%     if ~isempty(uid_motor_nbslice)&& ~isempty(uid_Dtk)% case of multilevel
%         NbSlice=str2num(get(t,get(t,uid_motor_nbslice,'contents'),'value'));
%         NbDti=NbSlice-1;
%     end
% end

if isempty(Dtj)% case of simple series
    timestamp=timestamp';
    t=set(t,uid_content_NbDti,'value',num2str(numel(timestamp)-1));% correct NbDti in the xml file 
    nbfield1=numel(timestamp);
    nbfield2=1;
else
    nbfieldi=(NbDti*numel(Dti)+1);
    nbfieldk=(NbDtk*numel(Dtk)+1);
    nbfield1=nbfieldi*nbfieldk;
    nbfield2=NbDtj*numel(Dtj)+1;
    NbFrames_xml=nbfield1*nbfield2;
%    if NbFrames_xml<numel(timestamp)
%        disp(['ERROR: size from xml ' num2str(NbFrame_xml) ' smaller than timestamp size ' num2str(numel(timestamp))])
%        return
%    end
%    if NbFrames_xml>numel(timestamp)
%        nbfield1=floor(numel(timestamp)/nbfield2);
%        nbfieldk=floor(nbfield1/nbfieldi);
%        nbfield1=nbfieldi*nbfieldk;
%        NbDtk=nbfieldk-1;
%        t=set(t,uid_content_NbDtk,'value',num2str(NbDtk));% correct NbDtk in the xml file (in practice numel(Dtk)=1;
%        timestamp=timestamp(1:nbfield1*nbfield2);
%        disp(['image record stopped before end: max index i= ' num2str(nbfield1)]);
%        timestamp=reshape(timestamp,nbfield2,nbfield1);
%    end
%    % check Dtj with respect to timestamp
%     timestamp=(reshape(timestamp,nbfield2,[]))';
%     diff_Dtj=diff(timestamp(1,:))-Dtj;
%     if max(abs(diff_Dtj))>min(Dtj)/1000
%         disp(['Dtj from xml file differs from time stamp by ' num2str(max(abs(diff_Dtj))) ', '])%'
%     else
%         disp('Dtj OK');
%     end
end

%% adjust Dti
% if NbDti+1>size(timestamp,1)
%     NbDti=size(timestamp,1)-1;
% end
% Dti_stamp=(timestamp(1+NbDti,1)-timestamp(1,1))/NbDti;
% Dti_stamp=(timestamp(1+NbDti,1)-timestamp(2,1))/(NbDti-1);
% t=set(t,uid_content_Dti,'value',num2str(Dti_stamp));%corret Dti
% if abs(Dti_stamp-Dti)>Dti/1000
%     disp([msg 'Dti from xml file corrected by ' num2str(Dti_stamp-Dti) ', ']);%'
% else
%     disp('Dti OK')
% end

%% adjust Dtk
if ~isempty(uid_Dtk)
    Dtk_stamp=(timestamp((NbDti+1)*NbDtk+1,1)-timestamp(1,1))/NbDtk;
    t=set(t,uid_content_Dtk,'value',num2str(Dtk_stamp));
    if abs(Dtk_stamp-Dtk)>Dtk/1000
        disp(['Dtk from xml file corrected by ' num2str(Dtk_stamp-Dtk)]);
    else
        disp('Dtk OK')
    end
    t=set(t,uid_content_Dtk,'value',num2str(Dtk_stamp));
end

%% save the new xml file
if ~isempty(newxml)
    save(t,newxml)
    [success,errormsg] = fileattrib(newxml,'+w','g');% allow writing access for the group of users
    if success==0
        disp({['warning: unable to set group write access to ' newxml ':']; errormsg});%error message for directory creation
        msg=errormsg;
    end
end