Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 1017) +++ /trunk/src/series/civ_input.m (revision 1018) @@ -713,6 +713,9 @@ if ischar(mode_list) mode_list={mode_list}; - end + end mode_value=get(handles.ListPairMode,'Value'); + if isempty(mode_value) + mode_value=1; + end mode=mode_list{mode_value}; end @@ -908,4 +911,7 @@ mode_list=get(handles.ListPairMode,'String'); mode_value=get(handles.ListPairMode,'Value'); + if isempty(mode_value) + mode_value=1; + end if isempty(mode_list) return @@ -1559,5 +1565,5 @@ if strcmp(NomType,'_1') NbSlice=i1_series(1,2,end); - set(handles.NbSlice,'String',num2str(NbSlice)) + set(handles.num_NbSlice,'String',num2str(NbSlice)) end set(hObject,'UserData',filemask);%store for future use Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 1017) +++ /trunk/src/series/extract_rdvision.m (revision 1018) @@ -200,13 +200,4 @@ 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} @@ -214,7 +205,9 @@ 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 + [success,errormsg] = copyfile(filexml,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.xml']); %copy the original xml file in the upper folder otherwise errormsg='input file extension must be .seq or .sqb'; @@ -240,5 +233,4 @@ SeqData.binrepertoire=regexprep(SeqData.binrepertoire,'\','/'); [tild,SeqData.binrepertoire,DirExt]=fileparts(SeqData.binrepertoire); - %SeqData.binrepertoire=[SeqData.binrepertoire DirExt]; end @@ -271,12 +263,6 @@ 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 + end + [nbfield1,nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml); %copy the xml file in the upper folder [XmlData,errormsg]=imadoc2struct(newxml);% check reading of the new xml file if ~isempty(errormsg) @@ -284,9 +270,7 @@ return end - if ~isequal(size(XmlData.Time(2:end,2:end)),size(reshape(timestamp(1:end),nbfield2,[])')) - disp(['size of record ' num2str(size(XmlData.Time(2:end,2:end))) ' does not fit with timestamp size ' num2str(size(reshape(timestamp(1:end),nbfield2,[])'))]) - return - end - difftime=XmlData.Time(2:end,2:end)-(reshape(timestamp(1:end),nbfield2,[]))'; + timestamp=timestamp(1:nbfield1*nbfield2); + timestamp=reshape(timestamp,nbfield2,nbfield1); + difftime=XmlData.Time(2:end,2:end)'-timestamp; disp(['time from xml and timestamp differ by ' num2str(max(max(abs(difftime))))]) if max(abs(difftime))>0.01 @@ -295,8 +279,8 @@ %% 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 +% 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 if nbfield2>1 @@ -329,11 +313,11 @@ %% remove binary files if transfer OK - if ~checkpreserve - for iview=1:size(Param.InputTable,1) - fullfile(RootPath,Param.InputTable{iview,2}) - source_dir=fullfile(RootPath,Param.InputTable{iview,2}); - [SUCCESS,MESSAGE]=rmdir(source_dir,'s') - end - end +% if ~checkpreserve +% for iview=1:size(Param.InputTable,1) +% fullfile(RootPath,Param.InputTable{iview,2}) +% source_dir=fullfile(RootPath,Param.InputTable{iview,2}); +% [SUCCESS,MESSAGE]=rmdir(source_dir,'s') +% end +% end delete(fullfile(RootPath,'Running.xml'))%delete the xml file to indicate that processing is finished @@ -451,23 +435,84 @@ -function [nbfield2,msg]=copyfile_modif(filexml,timestamp,newxml) +function [nbfield1,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 +%% read Dtk and NbDtk +NbDtk=1; %default +Dtk=[]; % default +uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk'); +uid_content_Dtk=get(t,uid_Dtk,'contents'); +if ~isempty(uid_content_Dtk) + Dtk=str2num(get(t,uid_content_Dtk,'value')); + uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); + uid_content_NbDtk=get(t,uid_NbDtk,'contents'); + if ~isempty(uid_content_NbDtk) + NbDtk=str2num(get(t,uid_content_NbDtk,'value')); + end +end + +%% read Dti and NbDti +NbDti=1; %default +Dti=[]; % default +uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti'); +uid_content_Dti=get(t,uid_Dti,'contents'); +if ~isempty(uid_content_Dti) + Dti=str2num(get(t,uid_content_Dti,'value')); + uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti'); + uid_content_NbDti=get(t,uid_NbDti,'contents'); + if ~isempty(uid_content_NbDti) + NbDti=str2num(get(t,uid_content_NbDti,'value')); + end +end + +%% read Dtj and NbDtj +NbDtj=1; %default +Dtj=[]; % default uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj'); -uid_content=get(t,uid_Dtj,'contents'); -Dtjstring=get(t,uid_content,'value'); -if isempty(Dtjstring) +uid_content_Dtj=get(t,uid_Dtj,'contents'); +if ~isempty(uid_content_Dtj) + Dtj=str2num(get(t,uid_content_Dtj,'value')); + uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); + uid_content_NbDtj=get(t,uid_NbDtj,'contents'); + if ~isempty(uid_content_NbDtj) + NbDtj=str2num(get(t,uid_content_NbDtj,'value')); + end +end + +%% correct NbDtj and NbDti (error from RDvision) +if NbDtj==numel(Dtj)% case of bursts + NbDtj=1; + uid_motor_nbslice=find(t,'ImaDoc/TranslationMotor/Nbslice'); + if ~isempty(uid_motor_nbslice)&& ~isempty(uid_Dtk)% case of multilevel + NbSlice=str2num(get(t,get(t,uid_motor_nbslice,'contents'),'value')); + NbDti=NbSlice-1; + end +end + +if isempty(Dtj)% case of simple series timestamp=timestamp'; - nbfield2=1; + t=set(t,uid_content_NbDti,'value',num2str(numel(timestamp)-1));% correct NbDti in the xml file else - Dtj=str2num(get(t,uid_content,'value')); - nbfield2=numel(Dtj)+1; + nbfieldi=(NbDti*numel(Dti)+1); + nbfieldk=(NbDtk*numel(Dtk)+1); + nbfield1=nbfieldi*nbfieldk; + nbfield2=NbDtj*numel(Dtj)+1; + NbFrames_xml=nbfield1*nbfield2; + if NbFrames_xmlnumel(timestamp) + nbfield1=floor(numel(timestamp)/nbfield2); + nbfieldk=floor(nbfield1/nbfieldi); + nbfield1=nbfieldi*nbfieldk; + NbDtk=nbfieldk-1; + t=set(t,uid_content_NbDtk,'value',num2str(NbDtk));% correct NbDtk in the xml file (in practice numel(Dtk)=1; + timestamp=timestamp(1:nbfield1*nbfield2); + disp(['image record stopped before end: max index i= ' num2str(nbfield1)]); + timestamp=reshape(timestamp,nbfield2,nbfield1); + end + % check Dtj with respect to timestamp timestamp=(reshape(timestamp,nbfield2,[]))'; diff_Dtj=diff(timestamp(1,:))-Dtj; @@ -478,22 +523,8 @@ 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; +t=set(t,uid_content_Dti,'value',num2str(Dti_stamp));%corret Dti if abs(Dti_stamp-Dti)>Dti/1000 disp([msg 'Dti from xml file corrected by ' num2str(Dti_stamp-Dti) ', ']);%' @@ -501,14 +532,9 @@ 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; + Dtk_stamp=(timestamp((NbDti+1)*NbDtk+1,1)-timestamp(1,1))/NbDtk; + t=set(t,uid_content_Dtk,'value',num2str(Dtk_stamp)); if abs(Dtk_stamp-Dtk)>Dtk/1000 disp(['Dtk from xml file corrected by ' num2str(Dtk_stamp-Dtk)]); @@ -519,4 +545,5 @@ end +%% save the new xml file save(t,newxml) [success,errormsg] = fileattrib(newxml,'+w','g');% allow writing access for the group of users