Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 1009) +++ /trunk/src/civ.m (revision 1010) @@ -1,7 +1,8 @@ -%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch) +%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch). OBSOLETE: REPLACED BY civ_series %------------------------------------------------------------------------ % provides an interface for the software menucivx % function varargout = civ(varargin) % provides an interface for the software menucivx +% OBSOLETE: REPLACED BY civ_series %======================================================================= Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1009) +++ /trunk/src/series.m (revision 1010) @@ -2045,8 +2045,13 @@ WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2); % estimated max time of an individual job for checkpoint disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes']) + if NbProcess>=8 + bigiojob_string=['+{type = ' char(39) 'bigiojob' char(39) '}/licence=1'];% char(39) is quote - bigiojob limit UVmat parallel launch on cluster to avoid saturation of disk access to data + else + bigiojob_string=''; + end oar_command=['oarsub -n UVmat_' ActionFullName ' '... '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '... '-l "/core=' num2str(NbCore)... - '+{type = ' char(39) 'bigiojob' char(39) '}/licence=1'... % char(39) is quote - bigiojob limit UVmat parallel launch on cluster + bigiojob_string... % char(39) is quote - bigiojob limit UVmat parallel launch on cluster ',walltime=' datestr(WallTimeTotal/24,13) '" '... '-E ' filename_errors ' '... Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 1009) +++ /trunk/src/series/civ_input.m (revision 1010) @@ -1516,5 +1516,5 @@ hchildren=get(hparent,'children'); handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel - +handle_NbSlice=findobj(hchildren,'tag','num_NbSlice');% look for the mask name box in the same panel testmask=0; if value @@ -1526,15 +1526,21 @@ ind_A=2; end - [nbslice, flag_mask]=get_mask(InputTable{ind_A,1},handles);% look for a mask with appropriate name - if isequal(flag_mask,1) - filemask=[num2str(nbslice) 'mask']; - testmask=1; - else % browse for a mask +% [nbslice, flag_mask]=get_mask(InputTable{ind_A,1},handles);% look for a mask with appropriate name +% if isequal(flag_mask,1) +% filemask=[num2str(nbslice) 'mask']; +% testmask=1; +% else % browse for a mask filemask= uigetfile_uvmat('pick a mask image file:',InputTable{ind_A,1},'image'); + [FilePath,FileName,Ext]=fileparts(filemask); + [RootPath,SubDir,RootFile,i1_series,i2,j1,j2,NomType]=find_file_series(FilePath,[FileName,Ext]); + if strcmp(NomType,'_1') + NbSlice=i1_series(1,2,end); + set(handle_NbSlice,'String',num2str(NbSlice)) + end set(hObject,'UserData',filemask);%store for future use if ~isempty(filemask) testmask=1; - end - end + end +% end end if testmask @@ -1542,7 +1548,11 @@ set(handles.Mask,'String',filemask) set(handles.CheckMask,'Value',1) + if strcmp(NomType,'_1') + set(handles.num_NbSlice,'Visible','on') + end else set(hObject,'Value',0); set(handle_txtbox,'Visible','off') + set(handles.num_NbSlice,'Visible','off') end set(handles.ConfigSource,'String','NEW') @@ -2375,2 +2385,25 @@ drawnow end + + + +function num_NbSlice_Callback(hObject, eventdata, handles) +% hObject handle to num_NbSlice (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of num_NbSlice as text +% str2double(get(hObject,'String')) returns contents of num_NbSlice as a double + + +% --- Executes during object creation, after setting all properties. +function num_NbSlice_CreateFcn(hObject, eventdata, handles) +% hObject handle to num_NbSlice (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 1009) +++ /trunk/src/series/civ_series.m (revision 1010) @@ -276,5 +276,5 @@ %%%%% MAIN LOOP %%%%%% -maskname='';% initiate the mask name +maskoldname='';% initiate the mask name FileType_A=''; FileType_B=''; @@ -440,10 +440,18 @@ Data.VarAttribute{4}.Role='vector_y'; Data.VarAttribute{5}.Role='warnflag'; + % case of mask if par_civ1.CheckMask&&~isempty(par_civ1.Mask) - if strcmp(maskname,par_civ1.Mask)% mask exist, not already read in civ1 + if isfield(par_civ1,'NbSlice') + [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask); + i1_mask=mod(i1-1,par_civ1.NbSlice)+1; + maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask); + else + maskname=Param.ActionInput.Civ1.Mask; + end + if strcmp(maskoldname,maskname)% mask exist, not already read in civ1 par_civ1.Mask=mask; %use mask already opened else try - par_civ1.Mask=imread(par_civ1.Mask);%update the mask, an store it for future use + par_civ1.Mask=imread(maskname);%update the mask, an store it for future use catch ME if ~isempty(ME.message) @@ -454,5 +462,5 @@ end mask=par_civ1.Mask; - maskname=par_civ1.Mask; + maskoldname=maskname; end end @@ -704,13 +712,29 @@ end end - if par_civ2.CheckMask&&~isempty(par_civ2.Mask) - if strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 + if par_civ2.CheckMask&&~isempty(par_civ2.Mask) + if isfield(par_civ2,'NbSlice') + [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask); + i1_mask=mod(i1-1,par_civ2.NbSlice)+1; + maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask); + else + maskname=Param.ActionInput.Civ2.Mask; + end + if strcmp(maskoldname,maskname)% mask exist, not already read in civ1 par_civ2.Mask=mask; %use mask already opened else - par_civ2.Mask=imread(par_civ2.Mask);%update the mask, and store it for future use + try + par_civ2.Mask=imread(maskname);%update the mask, an store it for future use + catch ME + if ~isempty(ME.message) + errormsg=['error reading input image: ' ME.message]; + disp_uvmat('ERROR',errormsg,checkrun) + return + end + end mask=par_civ2.Mask; - maskname=par_civ2.Mask; - end - end + maskoldname=maskname; + end + end + if CheckInputFile % else Dt given by par_civ2 if strcmp(Param.ActionInput.ListCompareMode,'displacement') Index: /trunk/src/series/extract_rdvision_times.m =================================================================== --- /trunk/src/series/extract_rdvision_times.m (revision 1010) +++ /trunk/src/series/extract_rdvision_times.m (revision 1010) @@ -0,0 +1,488 @@ +%'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 2008-2017, 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 + + + Index: unk/src/series/get_times_rdvision.m =================================================================== --- /trunk/src/series/get_times_rdvision.m (revision 1009) +++ (revision ) @@ -1,487 +1,0 @@ -%'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 2008-2017, 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)) - - - - % 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 - - - Index: /trunk/src/transform_field/signal_spectrum.m =================================================================== --- /trunk/src/transform_field/signal_spectrum.m (revision 1009) +++ /trunk/src/transform_field/signal_spectrum.m (revision 1010) @@ -1,5 +1,8 @@ % 'signal_spectrum': calculate and display power spectrum of the current field % operate on a 1D signal or the first dimension of a higher dimensional matrix (then average over other dimensions) -% this function aplies the Welch method and call the function of the matlab signal processing toolbox +% this function aplies the Welch method and calls the function of the matlab signal processing toolbox +% it calculates also the cospectrum with the signal shifted by one +% index, to remove noise effects assumed uncorrelated from one iteration to +% the next. % % OUTPUT: @@ -91,5 +94,9 @@ yindex=DataOut.TransformInput.IndexRange(2,:); y=Data.(YName)(yindex); + if size(DataOut.TransformInput.IndexRange,1)>=3 xindex=DataOut.TransformInput.IndexRange(3,:); + else + xindex=DataOut.TransformInput.IndexRange(2,:); + end x=Data.(XName)(xindex); haxes=findobj(huvmat,'Tag','PlotAxes'); Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1009) +++ /trunk/src/uvmat.m (revision 1010) @@ -5678,5 +5678,8 @@ %------------------------------------------------------------------------ check_view=get(handles.CheckViewObject,'Value'); - + hset_object=findobj(allchild(0),'tag','set_object'); + if ~isempty(hset_object) + delete(hset_object)% delete existing version of set_object + end if check_view %activate set_object IndexObj=get(handles.ListObject,'Value'); @@ -5713,8 +5716,8 @@ end else - hset_object=findobj(allchild(0),'tag','set_object'); - if ~isempty(hset_object) - delete(hset_object)% delete existing version of set_object - end +% hset_object=findobj(allchild(0),'tag','set_object'); +% if ~isempty(hset_object) +% delete(hset_object)% delete existing version of set_object +% end end