Index: trunk/src/series/civ_series.m =================================================================== --- trunk/src/series/civ_series.m (revision 1062) +++ trunk/src/series/civ_series.m (revision 1065) @@ -88,4 +88,6 @@ end end + % estimated CPUTime +Data.CPUTime=1; % 1 minute per field pair return end Index: trunk/src/series/extract_rdvision.m =================================================================== --- trunk/src/series/extract_rdvision.m (revision 1062) +++ trunk/src/series/extract_rdvision.m (revision 1065) @@ -26,5 +26,5 @@ % .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 +% .RunMode='local','background', 'cluster': type of function extract_rdvision.muse % % .IndexRange: set the file or frame indices on which the action must be performed @@ -44,5 +44,5 @@ % 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 +% Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.frextract_rdvision.m % % This file is part of the toolbox UVMAT. @@ -56,5 +56,5 @@ % 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. +% GNU General Public License (see LICENSE.txt) for more details.extract_rdvision.m %======================================================================= @@ -65,5 +65,5 @@ 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.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) @@ -71,5 +71,6 @@ 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.CPUTime=0.1;% expected time for writting one image ( in minute) + ParamOut.OutputDirExt='.extract';%set the output dir extensionextract_rdvision.m ParamOut.OutputSubDirMode='one'; %output folder given by the folder name of the first input line % detect the set of image folder @@ -80,6 +81,4 @@ 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; @@ -90,6 +89,4 @@ 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; @@ -98,5 +95,5 @@ InputTable{isel,3}=RootFile; InputTable{isel,4}='*'; - InputTable{isel,5}='.seq'; + InputTable{isel,5}='.seq';extract_rdvision.m end end @@ -114,5 +111,4 @@ if ischar(Param) Param=xml2struct(Param);% read Param as input file (batch case) -% checkrun=0; end disp(Param) @@ -144,9 +140,9 @@ 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 +% if ~isequal(FileInfo.NumberOfFrames,nbfield) +% disp_uvmat('WARNING',['the whole series of ' num2str(FileInfo.NumberOfextract_rdvision.mFrames) ' 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...') @@ -196,9 +192,4 @@ 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' @@ -210,10 +201,13 @@ 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 - if check_xml - [success,errormsg] = copyfile(filexml,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.xml']); %copy the original xml file in the upper folder + errormsg=''; + if isequal(Param.IndexRange.first_i,1) + + 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 + if check_xml + [success,errormsg] = copyfile(filexml,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.xml']); %copy the original xml file in the upper folder + end end otherwise @@ -267,28 +261,30 @@ % m.Data=data; %%%%%%% - timestamp=zeros(1,numel(m.Data)); - for ii=1: numel(m.Data) - timestamp(ii)=m.Data(ii).timestamp; - end - [nbfield1,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 - timestamp=timestamp(1:nbfield1*nbfield2); - 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 - - %% 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 - + 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) + [nbfield1,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 + timestamp=timestamp(1:nbfield1*nbfield2); + 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 + % 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 + else + [nbfield1,nbfield2,msg]=copyfile_modif(filexml,timestamp,''); + end if nbfield2>1 NomTypeNew='_1_1'; @@ -297,5 +293,5 @@ end - [BinList,errormsg]=binread_rdv_series(RootPath,SeqData,m.Data,nbfield2,NomTypeNew); + [BinList,errormsg]=binread_rdv_series(RootPath,SeqData,m.Data,nbfield2,NomTypeNew,Param.IndexRange.first_i,Param.IndexRange.last_i); if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) @@ -304,17 +300,18 @@ % check the existence of the expected output image files (from the xml) + FileDir=SeqData.sequencename; FileDir=regexprep(FileDir,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180' - for i1=1:numel(timestamp)/nbfield2 - for j1=1:nbfield2 - OutputFile=fullfile_uvmat(RootPath,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode - try - A=imread(OutputFile);% check image reading (stop if error) - catch ME - disp(['checking ' OutputFile]) - disp(ME.message) - end - end - end +% for i1=1:numel(timestamp)/nbfield2 +% for j1=1:nbfield2 +% OutputFile=fullfile_uvmat(RootPath,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode +% try +% A=imread(OutputFile);% check image reading (stop if error) +% catch ME +% disp(['checking ' OutputFile]) +% disp(ME.message) +% end +% end +% end end @@ -333,5 +330,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -function [BinList,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew) +function [BinList,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew,first,last) % BINREAD_RDV Permet de lire les fichiers bin g???n???r???s par Hiris ??? partir du % fichier seq associ???. @@ -387,5 +384,6 @@ end bin_file_counter=0; -for ii=1:SeqData.nb_frames +%for ii=1:SeqData.nb_frames +for ii=first:last j1=[]; if ~isequal(nbfield2,1) @@ -422,6 +420,8 @@ 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 @@ -559,11 +559,12 @@ %% save the new xml file -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 - - - +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 + +