%'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 use % % .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 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.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. %======================================================================= 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=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.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)); % InputTable=cell(numel(ListDir),5); % InputTable(:,2)=ListDir'; 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$'); seq_index=find(~cellfun('isempty',detect_seq),1); if ~isempty(seq_index) % msgbox_uvmat('ERROR',['not seq file in ' ListDir{ilist} ': please check the input folders']) % else isel=isel+1; InputTable{isel,1}=RootPath; InputTable{isel,2}=ListDir{ilist}; RootFile=regexprep(ListCellSub{1,seq_index},'.seq$',''); 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 .... return end ParamOut=[]; %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% %% read input parameters from an xml file if input is a file name (batch mode) checkrun=1; if ischar(Param) Param=xml2struct(Param);% read Param as input file (batch case) checkrun=0; end 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); %OutputDir=[Param.OutputSubDir Param.OutputDirExt]; % 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') if ~isequal(FileInfo.NumberOfFrames,nbfield) disp_uvmat('WARNING',['the whole series of ' num2str(FileInfo.NumberOfFrames) ' images must be extracted at once'],checkrun) %rmfield(OutputDir) % return end %% 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) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % RootPath=Param.InputTable(:,1); % RootFile=Param.InputTable(:,3); % SubDir=Param.InputTable(:,2); % NomType=Param.InputTable(:,4); % FileExt=Param.InputTable(:,5); % [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); % if size(time,1)>1 % diff_time=max(max(diff(time))); % if diff_time>0 % disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) % end % end % % nbfield2=size(time,1); checkpreserve=0;% if =1, will npreserve the original images, else it erases them at the end for iview=1:size(Param.InputTable,1) 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') break end end if ~exist(filexml,'file') disp_uvmat('ERROR',[filexml ' missing'],checkrun) return end newxml=fullfile(RootPath,Param.InputTable{iview,3}); newxml=regexprep(newxml,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180' newxml=[newxml '.xml']; %copyfile_modif(filexml,newxml); %copy the xml file in the upper folder %[XmlData,errormsg]=imadoc2struct(newxml); % nbfield2=size(XmlData.Time,2)-1; % if nbfield2>1 % NomTypeNew='_1_1'; % else % NomTypeNew='_1'; % end %% get the names of .seq and .sqb files switch Param.InputTable{iview,5} case {'.seq','.sqb'} filename_seq=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.seq']); filename_sqb=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.sqb']); logdir=[Param.OutputSubDir Param.OutputDirExt]; [success,errormsg] = copyfile(filename_seq,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.seq']); %copy the seq file in the upper folder [success,errormsg] = copyfile(filename_sqb,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.sqb']); %copy the sqb file in the upper folder otherwise errormsg='input file extension must be .seq or .sqb'; end if ~exist(filename_seq,'file') errormsg=[filename_seq ' does not exist']; end if ~isempty(errormsg) disp_uvmat('ERRROR',errormsg,checkrun); return end %% get data from .seq file s=ini2struct(filename_seq); SeqData=s.sequenceSettings; SeqData.width=str2double(SeqData.width); SeqData.height=str2double(SeqData.height); SeqData.bytesperpixel=str2double(SeqData.bytesperpixel); SeqData.nb_frames=str2double(s.sequenceSettings.numberoffiles); if isempty(SeqData.binrepertoire)%used when binrepertoire empty, strange feature of rdvision SeqData.binrepertoire=regexprep(s.sequenceSettings.bindirectory,'\\$','');%tranform Windows notation to Linux SeqData.binrepertoire=regexprep(SeqData.binrepertoire,'\','/'); [tild,binrepertoire,DirExt]=fileparts(SeqData.binrepertoire); SeqData.binrepertoire=[SeqData.binrepertoire DirExt]; 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=[111 114:211];%indices of bin files % w=1024;%w=width of images in pixels % h=1024;%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=32; %nbre of images of each camera in a bin file % for ii=1:32*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).timestamp=0.2*(ii-1); % end % m.Data=data; %%%%%%% timestamp=zeros(1,numel(m.Data)); for ii=1: numel(m.Data) timestamp(ii)=m.Data(ii).timestamp; % j1=1; % if ~isequal(nbfield2,1) % j1=mod(ii-1,nbfield2)+1; % end % i1=floor((ii-1)/nbfield2)+1; %diff_time(i1,j1)= timestamp(ii)-XmlData.Time(i1+1,j1+1); end [nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml); %copy the xml file in the upper folder [XmlData,errormsg]=imadoc2struct(newxml);% check reading of the new xml file if ~isempty(errormsg) disp(errormsg) return end difftime=XmlData.Time(2:end,2:end)-(reshape(timestamp,nbfield2,[]))'; 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 %% checking consistency with the xml file if ~isequal(SeqData.nb_frames,numel(timestamp)) disp_uvmat('ERRROR',['inconsistent number of images ' num2str(SeqData.nb_frames) ' with respect to the xml file: ' num2str(numel(timestamp))] ,checkrun); return end disp ('max time difference xml and timestamps (IN SEC.)') max(abs(difftime)) end % check the existence of the expected output image files (from the xml) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %--------- reads a series of bin files %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function [BinList,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew) % 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) 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 j1=[]; if ~isequal(nbfield2,1) j1=mod(ii-1,nbfield2)+1; end i1=floor((ii-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 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 imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images disp([OutputFile ' written']); % [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 function [nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml) msg=''; t=xmltree(filexml); %% correct NbDtj uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); uid_content=get(t,uid_NbDtj,'contents'); t=set(t,uid_content,'value','1');% set NbDtj to 1 (correct error in the xml file) %% check Dtj uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj'); uid_content=get(t,uid_Dtj,'contents'); Dtjstring=get(t,uid_content,'value'); if isempty(Dtjstring) timestamp=timestamp'; nbfield2=1; else Dtj=str2num(get(t,uid_content,'value')); nbfield2=numel(Dtj)+1; 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 %% correct NbDti NbDti=size(timestamp,1)-1; %default for series or burst uid_motor_nbslice=find(t,'ImaDoc/TranslationMotor/Nbslice'); uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); if ~isempty(uid_motor_nbslice)&& ~isempty(uid_NbDtk) uid_content=get(t,uid_motor_nbslice,'contents'); NbSlice=str2num(get(t,uid_content,'value')); NbDti=NbSlice-1; uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti'); uid_content=get(t,uid_NbDti,'contents'); t=set(t,uid_content,'value',num2str(NbDti)); end %% adjust Dti uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti'); uid_content=get(t,uid_Dti,'contents'); Dti=str2num(get(t,uid_content,'value')); Dti_stamp=(timestamp(1+NbDti,1)-timestamp(1,1))/NbDti; if abs(Dti_stamp-Dti)>Dti/1000 disp([msg 'Dti from xml file corrected by ' num2str(Dti_stamp-Dti) ', ']);%' else disp('Dti OK') end t=set(t,uid_content,'value',num2str(Dti_stamp)); %% adjust Dtk uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk'); if ~isempty(uid_Dtk) uid_content_Dtk=get(t,uid_Dtk,'contents'); Dtk=str2num(get(t,uid_content_Dtk,'value')); uid_content_NbDtk=get(t,uid_NbDtk,'contents'); NbDtk=str2num(get(t,uid_content_NbDtk,'value')); Dtk_stamp=(timestamp(end-NbDti,1)-timestamp(1,1))/NbDtk; 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(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