%'relabel_i_j': relabel an image series with two indices, and correct errors from the RDvision transfer program %------------------------------------------------------------------------ % function ParamOut=relabel_i_j(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=relabel_i_j(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='one'; ...%nbre of slices, 'one' 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='';%set the output dir extension if size(Param.InputTable,1)>1 msgbox_uvmat('WARNING', 'this function acts only on the first input file line') end 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); RootFile=Param.InputTable(:,3); SubDir=Param.InputTable(:,2); NomType=Param.InputTable(:,4); FileExt=Param.InputTable(:,5); % get the set of input file names (cell array filecell), and the lists of % input file or frame indices i1_series,i2_series,j1_series,j2_series [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); % numbers of slices and file indices nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) nbfield_i=size(i1_series{1},2); %nb of fields for the i index nbfield=nbfield_j*nbfield_i; %total number of fields %determine the file type on each line from the first input file ImageTypeOptions={'image','multimage','mmreader','video'}; if ~exist(filecell{1,1}','file') msgbox_uvmat('ERROR',['the first input file ' filecell{1,1} ' does not exist']) return end [FileInfo{1},MovieObject{1}]=get_file_info(filecell{1,1}); FileType{1}=FileInfo{1}.FileType; CheckImage=~isempty(find(strcmp(FileType{1},ImageTypeOptions)));% =1 for images %% 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 '.' filexml=[fullfile(RootPath{1},SubDirBase) '.xml'];%new convention: xml at the level of the image folder if ~exist(filexml,'file') filexml=[fullfile(RootPath{1},SubDir{1},RootFile{1}) '.xml']; % old convention: xml inside the image folder if ~exist(filexml,'file') filexml=[fullfile(RootPath{1},SubDir{1},RootFile{1}) '.civ']; % very old convention: .civ file if ~exist(filexml,'file') filexml=''; end end end XmlData=[]; if ~isempty(filexml) [XmlData,error]=imadoc2struct_special(filexml); end if isfield(XmlData,'Time') itime=itime+1; timecell{itime}=XmlData.Time; end if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord') NbSlice_calib{1}=size(XmlData.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform if ~isequal(NbSlice_calib{1},NbSlice_calib{1}) msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); end end %% check coincidence in time for several input file series % not relevant %% coordinate transform or other user defined transform %not relevant %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% % EDIT FROM HERE %% Set field names and velocity types % not relevant here %% Initiate output fields % not relevant here %% interactive input of specific parameters (for RDvision system) display('RDvision system') first_label=0; %image numbers start from 0 if ~CheckImage || ~strcmp(NomType{1},'_000001') msgbox_uvmat('WARNING','the input is not a file from RDvision: this function relabel_i_j has no action');%error message for directory creation return else answer=msgbox_uvmat('','this function will relabel the file series from RDvision from and correct the xml file');%error message for directory creation if ~strcmp(answer,'Yes') return end end %% copy and adapt the xml file NomTypeNew='_1_1'; if ~isempty(XmlData) t=xmltree(filexml); %update information on the first image name in the series uid_Heading=find(t,'ImaDoc/Heading'); if isempty(uid_Heading) [t,uid_Heading]=add(t,1,'element','Heading'); end uid_ImageName=find(t,'ImaDoc/Heading/ImageName'); j1=[]; if ~isempty(j1_series{1}) j1=j1_series{1}; end ImageName=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},'_1_1',i1_series{1}(1),[],j1); [pth,ImageName]=fileparts(ImageName); ImageName=[ImageName '.png']; if isempty(uid_ImageName) [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); end uid_value=children(t,uid_ImageName); if isempty(uid_value) t=add(t,uid_ImageName,'chardata',ImageName);%indicate name of the first image, with ;png extension else t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension end %%%% correction RDvision %%%% if isfield(XmlData,'NbDtj') uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); uid_value=children(t,uid_NbDtj); if ~isempty(uid_value) t=set(t,uid_value(1),'value',num2str(XmlData.NbDtj)); end end if isfield(XmlData,'NbDtk') uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); uid_value=children(t,uid_NbDtk); if ~isempty(uid_value) t=set(t,uid_value(1),'value',num2str(XmlData.NbDtk)); end end if isempty(j1_series{1}) && isfield(XmlData,'NbDti') uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti'); t=add(t,uid_Dti,'chardata',num2str(XmlData.Dti)); uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti'); t=add(t,uid_NbDti,'chardata',num2str(XmlData.NbDti)); uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); t=delete(t,uid_NbDtj); t=delete(t,uid_NbDtk); uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj'); uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk'); t=delete(t,uid_Dtj); t=delete(t,uid_Dtk); NomTypeNew='_1'; end SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.' filexml_new=[fullfile(RootPath{1},SubDirBase) '.xml']; save(t,filexml_new) end %% main loop on images %j1=[];%default nbfield2=1; if isfield(XmlData,'Time') nbfield2=size(XmlData.Time,2); end for ifile=1:nbfield update_waitbar(WaitbarHandle,ifile/nbfield) if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') break end filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile)); j1=[]; if ~isequal(nbfield2,1) j1=mod(ifile-1+first_label,nbfield2)+1; end i1=floor((ifile-1+first_label)/nbfield2)+1; filename_new=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomTypeNew,i1,[],j1); try movefile(filename,filename_new); [s,errormsg] = fileattrib(filename_new,'-w','a'); %set images to read only '-w' for all users ('a') if ~s msgbox_uvmat('ERROR',errormsg); return end catch ME msgbox_uvmat('ERROR',ME.message); 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