Index: /trunk/src/series/extract_multitif.m =================================================================== --- /trunk/src/series/extract_multitif.m (revision 930) +++ /trunk/src/series/extract_multitif.m (revision 930) @@ -0,0 +1,171 @@ +%'ima2netcdf': read image series and transform to netcdf +%------------------------------------------------------------------------ + + +% function ParamOut=ima2netcdf(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 2008-2016, 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=ima2netcdf(Param) + +%%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% +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='on'; % edit box nbre of slices made active + 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='.png';%set the output dir extension + ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice + + %% root input file(s) and type + % check the existence of the first file in the series + first_j=[];% note that the function will propose to cover the whole range of indices + if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end + last_j=[]; + if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end + PairString=''; + if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end + [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); + FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... + Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); + if ~exist(FirstFileName,'file') + msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) + else + [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); + LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... + Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); + if ~exist(FirstFileName,'file') + msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) + end + end + + %% check the validity of input file types + ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images) + FileInfo=get_file_info(FirstFileName); + FileType=FileInfo.FileType; + CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions), 1));% =1 for images + if ~CheckImage + msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not an image']) + return + end + + return +end +%%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% + +%% read input parameters from an xml file if input is a file name (batch mode) +checkrun=1; +RUNHandle=[]; +WaitbarHandle=[]; +if ischar(Param) + Param=xml2struct(Param);% read Param as input file (batch case) + checkrun=0; +else +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 +end + +%% list of input images +DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2}); +ListStruct=dir(DirImages); +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 +ListFile=ListCells(1,find(~check_dir & ~check_bad)); + +% %% create the netcdf file with name flname in format NETCDF4 + OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); + +% cmode = netcdf.getConstant('NETCDF4'); +% cmode = bitor(cmode, netcdf.getConstant('CLASSIC_MODEL')); +% cmode = bitor(cmode, netcdf.getConstant('CLOBBER')); +% nc = netcdf.create(fullfile(OutputDir,'images.nc'), cmode); + +%% Main loop +ImagesPerLevel=100;%100; +count=0; +%count=933;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 67->_11_1 +%count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: +%% loop on the files +for ifile=1:numel(ListFile) + update_waitbar(WaitbarHandle,ifile/numel(ListFile)) + if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') + disp('program stopped by user') + break + end + ImageName=fullfile(DirImages,ListFile{ifile}); + NbFrames=numel(imfinfo(ImageName)); + % loop on the frames within the tiff file + for iframe=1:NbFrames + A=imread(ImageName,iframe); + count=count+1; + if isequal(ImagesPerLevel,1)% mode series + + OutputFile=fullfile(OutputDir,['img_' num2str(count) '.png']); + else % mode multilevel or volume (indices i and j) + i_index=fix(count/ImagesPerLevel)+1; + j_index=mod(count,ImagesPerLevel)+1; + OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); + end + imwrite(A,OutputFile,'BitDepth',16) + end +end + + Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 929) +++ /trunk/src/series/extract_rdvision.m (revision 930) @@ -153,5 +153,5 @@ end t=xmltree; -%%% A REMETTREE %%%%%%%%%%%%%%%%%%%%% + save(t,fullfile(RootPath,'Running.xml'))%create an xml file to indicate that processing takes place @@ -194,17 +194,18 @@ return end - [XmlData,errormsg]=imadoc2struct(filexml); + newxml=fullfile(RootPath,Param.InputTable{iview,3}); newxml=regexprep(newxml,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180' newxml=[newxml '.xml']; - [success,errormsg] = copyfile(filexml,newxml); %copy the xml file in the upper folder - - nbfield2=size(XmlData.Time,2)-1; - if nbfield2>1 - NomTypeNew='_1_1'; - else - NomTypeNew='_1'; - end + %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} @@ -212,5 +213,5 @@ 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.InputTable{1,2} .extract]; + 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 @@ -240,11 +241,5 @@ SeqData.binrepertoire=[SeqData.binrepertoire DirExt]; end - - %% checking consistency with the xml file - [npi,npj]=size(XmlData.Time); - if ~isequal(SeqData.nb_frames,(npi-1)*(npj-1)) - disp_uvmat('ERRROR',['inconsistent number of images ' num2str(SeqData.nb_frames) ' with respect to the xml file: ' num2str((npi-1)*(npj-1))] ,checkrun); - return - end + %% reading the .sqb file @@ -273,27 +268,28 @@ 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 - time_diff_max=max(diff_time'); - time_diff_min=min(diff_time'); - if max(time_diff_max)>0.005 - disp(['WARNING:timestamps exceeds xml time by' num2str(max(time_diff_max))]) - checkpreserve=1; - elseif min(time_diff_min)<-0.005 - disp(['timestamps is lower than xml time by' num2str(min(time_diff_min))]) - checkpreserve=1; +% 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 + if nbfield2>1 + NomTypeNew='_1_1'; else - disp('CONFIRMATION:time from xml file correct within better than 5 ms') - end - if checkpreserve - disp( 'max and min of timestamp-xml time for each index i:') - disp(time_diff_max) - disp(time_diff_min) - end + NomTypeNew='_1'; + end + [BinList,errormsg]=binread_rdv_series(RootPath,SeqData,m.Data,nbfield2,NomTypeNew); if ~isempty(errormsg) @@ -301,4 +297,5 @@ return end + % check the existence of the expected output image files (from the xml) FileDir=SeqData.sequencename; @@ -314,8 +311,9 @@ %% remove binary files if transfer OK if ~checkpreserve - for ibin=1:numel(BinList) - delete(BinList{ibin}) + for iview=1:size(Param.InputTable,1) + fullfile(RootPath,Param.InputTable{iview,2}) + + [SUCCESS,MESSAGE]=rmdir(fullfile(RootPath,Param.InputTable{iview,2}),'s') end - rmdir(fullfile(RootPath,Param.InputTable{iview,2})) end delete(fullfile(RootPath,'Running.xml'))%delete the xml file to indicate that processing is finished @@ -323,4 +321,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %--------- reads a series of bin files + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function [BinList,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew) @@ -349,4 +348,6 @@ fid=0; errormsg=''; +BinList={}; + classname=sprintf('uint%d',SeqData.bytesperpixel*8); @@ -424,354 +425,70 @@ -% for ifile=1:nbfield -% update_waitbar(WaitbarHandle,ifile/nbfield) -% if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') -% disp('program stopped by user') -% break -% end -% [A,FileInfo,timestamps]=read_rdvision(filename,ifile); -% if ifile==1 -% classA=class(A); -% if strcmp(classA,'uint8') -% BitDepth=8; -% else -% BitDepth=16; -% end -% end -% j1=[]; -% if ~isequal(nbfield2,1) -% j1=mod(ifile-1+first_label,nbfield2)+1; -% end -% i1=floor((ifile-1+first_label)/nbfield2)+1; -% OutputFile=fullfile_uvmat(RootPath{1},OutputDir,'img','.png',NomTypeNew,i1,[],j1); -% 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 -% disp_uvmat('ERROR',ME.message,checkrun); -% return -% end -% -% end - -%'imadoc2struct_special': reads the xml file for image documentation -%------------------------------------------------------------------------ -% function [s,errormsg]=imadoc2struct_special(ImaDoc,option) -% -% OUTPUT: -% s: structure representing ImaDoc -% s.Heading: information about the data hierarchical structure -% s.Time: matrix of times -% s.TimeUnit -% s.GeometryCalib: substructure containing the parameters for geometric calibration -% errormsg: error message -% -% INPUT: -% ImaDoc: full name of the xml input file with head key ImaDoc -% option: ='GeometryCalib': read the data of GeometryCalib, including source point coordinates - -function [s,errormsg]=imadoc2struct_special(ImaDoc,option) - -%% default input and output -if ~exist('option','var') - option='*'; -end -errormsg=[];%default -s.Heading=[];%default -s.Time=[]; %default -s.TimeUnit=[]; %default -s.GeometryCalib=[]; -tsai=[];%default - -%% opening the xml file -if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist -try - t=xmltree(ImaDoc); -catch - errormsg={[ImaDoc ' is not a valid xml file']; lasterr}; - display(errormsg); - return -end -uid_root=find(t,'/ImaDoc'); -if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file - - -%% Heading -uid_Heading=find(t,'/ImaDoc/Heading'); -if ~isempty(uid_Heading), - uid_Campaign=find(t,'/ImaDoc/Heading/Campaign'); - uid_Exp=find(t,'/ImaDoc/Heading/Experiment'); - uid_Device=find(t,'/ImaDoc/Heading/Device'); - uid_Record=find(t,'/ImaDoc/Heading/Record'); - uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName'); - s.Heading.Campaign=get(t,children(t,uid_Campaign),'value'); - s.Heading.Experiment=get(t,children(t,uid_Exp),'value'); - s.Heading.Device=get(t,children(t,uid_Device),'value'); - if ~isempty(uid_Record) - s.Heading.Record=get(t,children(t,uid_Record),'value'); - end - s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value'); -end - -%% Camera and timing -if strcmp(option,'*') || strcmp(option,'Camera') - uid_Camera=find(t,'/ImaDoc/Camera'); - if ~isempty(uid_Camera) - uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize'); - if ~isempty(uid_ImageSize); - ImageSize=get(t,children(t,uid_ImageSize),'value'); - xindex=findstr(ImageSize,'x'); - if length(xindex)>=2 - s.Npx=str2double(ImageSize(1:xindex(1)-1)); - s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1)); - end - end - uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit'); - if ~isempty(uid_TimeUnit) - s.TimeUnit=get(t,children(t,uid_TimeUnit),'value'); - end - uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming'); - if ~isempty(uid_BurstTiming) - for k=1:length(uid_BurstTiming) - subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming - % reading Dtk - Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1); - Dtj=get_value(subt,'/BurstTiming/Dtj',[]); - Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') - NbDtj=get_value(subt,'/BurstTiming/NbDtj',[]); - %%%% correction RDvision %%%% -% NbDtj=NbDtj/numel(Dtj); -% s.NbDtj=NbDtj; -% %%%% - Dti=get_value(subt,'/BurstTiming/Dti',[]); - NbDti=get_value(subt,'/BurstTiming/NbDti',1); - %%%% correction RDvision %%%% - if isempty(Dti)% series - Dti=Dtj; - NbDti=NbDtj; - Dtj=[]; - s.Dti=Dti; - s.NbDti=NbDti; - else - % NbDtj=NbDtj/numel(Dtj);%bursts - if ~isempty(NbDtj) - s.NbDtj=NbDtj/numel(Dtj);%bursts; - else - s.NbDtj=1; - end - end - %%%% %%%% - Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') - - Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit - if ~isempty(Dti) - Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times - Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals Dti - end - if ~isempty(Dtj) - Dtj=reshape(Dtj'*ones(1,s.NbDtj),1,s.NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times - Dtj=[0 Dtj]; - Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj - end - % reading Dtk - Dtk=get_value(subt,'/BurstTiming/Dtk',[]); - NbDtk=get_value(subt,'/BurstTiming/NbDtk',1); - %%%% correction RDvision %%%% - if ~isequal(NbDtk,1) - NbDtk=-1+(NbDtk+1)/(NbDti+1); - end - s.NbDtk=NbDtk; - %%%%% - if isempty(Dtk) - s.Time=[s.Time;Time_val]; - else - for kblock=1:NbDtk+1 - Time_val_k=Time_val+(kblock-1)*Dtk; - s.Time=[s.Time;Time_val_k]; - end - end - end - end - end -end - -%% motor -if strcmp(option,'*') || strcmp(option,'GeometryCalib') - uid_subtree=find(t,'/ImaDoc/TranslationMotor'); - if length(uid_subtree)==1 - subt=branch(t,uid_subtree);%subtree under GeometryCalib - [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]); - end -end -%% geometric calibration -if strcmp(option,'*') || strcmp(option,'GeometryCalib') - uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib'); - if ~isempty(uid_GeometryCalib) - if length(uid_GeometryCalib)>1 - errormsg=['More than one GeometryCalib in ' filecivxml]; - return - end - subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib - cont=get(subt,1,'contents'); - if ~isempty(cont) - uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType'); - if isequal(length(uid_CalibrationType),1) - tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value'); - end - uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit'); - if isequal(length(uid_CoordUnit),1) - tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value'); - end - uid_fx_fy=find(subt,'/GeometryCalib/fx_fy'); - focal=[];%default fro old convention (Reg Wilson) - if isequal(length(uid_fx_fy),1) - tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value')); - else %old convention (Reg Wilson) - uid_focal=find(subt,'/GeometryCalib/focal'); - uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy'); - uid_sx=find(subt,'/GeometryCalib/sx'); - if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx) - dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value')); - sx=str2num(get(subt,children(subt,uid_sx),'value')); - focal=str2num(get(subt,children(subt,uid_focal),'value')); - tsai.fx_fy(1)=sx*focal/dpx_dpy(1); - tsai.fx_fy(2)=focal/dpx_dpy(2); - end - end - uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy'); - if ~isempty(uid_Cx_Cy) - tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value')); - end - uid_kc=find(subt,'/GeometryCalib/kc'); - if ~isempty(uid_kc) - tsai.kc=str2double(get(subt,children(subt,uid_kc),'value')); - else %old convention (Reg Wilson) - uid_kappa1=find(subt,'/GeometryCalib/kappa1'); - if ~isempty(uid_kappa1)&& ~isempty(focal) - kappa1=str2double(get(subt,children(subt,uid_kappa1),'value')); - tsai.kc=-kappa1*focal*focal; - end - end - uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz'); - if ~isempty(uid_Tx_Ty_Tz) - tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value')); - end - uid_R=find(subt,'/GeometryCalib/R'); - if ~isempty(uid_R) - RR=get(subt,children(subt,uid_R),'value'); - if length(RR)==3 - tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})]; - end - end - - %look for laser plane definitions - uid_Angle=find(subt,'/GeometryCalib/PlaneAngle'); - uid_Pos=find(subt,'/GeometryCalib/SliceCoord'); - if isempty(uid_Pos) - uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention - end - if ~isempty(uid_Angle) - tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value')); - end - if ~isempty(uid_Pos) - for j=1:length(uid_Pos) - tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value')); - end - uid_DZ=find(subt,'/GeometryCalib/SliceDZ'); - uid_NbSlice=find(subt,'/GeometryCalib/NbSlice'); - if ~isempty(uid_DZ) && ~isempty(uid_NbSlice) - DZ=str2double(get(subt,children(subt,uid_DZ),'value')); - NbSlice=get(subt,children(subt,uid_NbSlice),'value'); - if isequal(NbSlice,'volume') - tsai.NbSlice='volume'; - NbSlice=NbDtj+1; - else - tsai.NbSlice=str2double(NbSlice); - end - tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1]; - end - end - tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]); - tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n'); - tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]); - tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1); - - if strcmp(option,'GeometryCalib') - tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]); - end - s.GeometryCalib=tsai; - end - end -end - -%-------------------------------------------------- -% read a subtree -% INPUT: -% t: xltree -% head_element: head elelemnt of the subtree -% Data, structure containing -% .Key: element name -% .Type: type of element ('charg', 'float'....) -% .NbOccur: nbre of occurrence, NaN for un specified number -function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest) -%-------------------------------------------------- -s=[];%default -errormsg=''; -head_element=get(subt,1,'name'); - cont=get(subt,1,'contents'); - if ~isempty(cont) - for ilist=1:length(Data) - uid_key=find(subt,[head_element '/' Data{ilist}]); - if ~isequal(length(uid_key),NbOccur(ilist)) - errormsg=['wrong number of occurence for ' Data{ilist}]; - return - end - for ival=1:length(uid_key) - val=get(subt,children(subt,uid_key(ival)),'value'); - if ~NumTest(ilist) - eval(['s.' Data{ilist} '=val;']); - else - eval(['s.' Data{ilist} '=str2double(val);']) - end - end - end - end - - -%-------------------------------------------------- -% read an xml element -function val=get_value(t,label,default) -%-------------------------------------------------- -val=default; -uid=find(t,label);%find the element iud(s) -if ~isempty(uid) %if the element named label exists - uid_child=children(t,uid);%find the children - if ~isempty(uid_child) - data=get(t,uid_child,'type');%get the type of child - if iscell(data)% case of multiple element - for icell=1:numel(data) - val_read=str2num(get(t,uid_child(icell),'value')); - if ~isempty(val_read) - val(icell,:)=val_read; - end - end -% val=val'; - else % case of unique element value - val_read=str2num(get(t,uid_child,'value')); - if ~isempty(val_read) - val=val_read; - else - val=get(t,uid_child,'value');%char string data - end - end - end -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'); +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 + +%% correct NbDti +NbDti=size(timestamp,1); %default for series or burst +uid_motor_nbslice=find(t,'ImaDoc/TranslationMotor/Nbslice'); +if ~isempty(uid_motor_nbslice) + 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_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); +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([msg '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) + + + + Index: /trunk/src/struct2nc.m =================================================================== --- /trunk/src/struct2nc.m (revision 929) +++ /trunk/src/struct2nc.m (revision 930) @@ -35,18 +35,18 @@ %======================================================================= -function errormsg=struct2nc(flname,Data) -if ~ischar(flname) - errormsg='invalid input for the netcf file name'; - return -end +function [errormsg,nc]=struct2nc(flname,Data,action) +nc=[]; +% if ~ischar(flname) +% errormsg='invalid input for the netcf file name'; +% return +% end if ~exist('Data','var') errormsg='no data input for the netcdf file'; return end -FilePath=fileparts(flname); -if ~strcmp(FilePath,'') && ~exist(FilePath,'dir') - errormsg=['directory ' FilePath ' needs to be created']; - return -end +if ~exist('action','var') + action='one_input'; %fill the file with data and close it +end + %% check the validity of the input field structure @@ -59,8 +59,17 @@ %% create the netcdf file with name flname in format NETCDF4 -cmode = netcdf.getConstant('NETCDF4'); -cmode = bitor(cmode, netcdf.getConstant('CLASSIC_MODEL')); -cmode = bitor(cmode, netcdf.getConstant('CLOBBER')); -nc = netcdf.create(flname, cmode); +if ischar(flname) + FilePath=fileparts(flname); + if ~strcmp(FilePath,'') && ~exist(FilePath,'dir') + errormsg=['directory ' FilePath ' needs to be created']; + return + end + cmode = netcdf.getConstant('NETCDF4'); + cmode = bitor(cmode, netcdf.getConstant('CLASSIC_MODEL')); + cmode = bitor(cmode, netcdf.getConstant('CLOBBER')); + nc = netcdf.create(flname, cmode); +else + nc=flname; +end %% write global constants @@ -159,6 +168,7 @@ end end +if strcmp(action,'one_input') netcdf.close(nc) - +end %'check_field_structure': check the validity of the field struture representation consistant with the netcdf format Index: /trunk/src/xml2struct.m =================================================================== --- /trunk/src/xml2struct.m (revision 929) +++ /trunk/src/xml2struct.m (revision 930) @@ -13,5 +13,6 @@ %======================================================================= -% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France +% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France/.fsnet/project/coriolis/2016/16CIRCUMPOLAR/EXP07/2016-03-08T + % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr