Index: /trunk/src/series/relabel_i_j.m =================================================================== --- /trunk/src/series/relabel_i_j.m (revision 554) +++ /trunk/src/series/relabel_i_j.m (revision 555) @@ -1,5 +1,5 @@ %'relabel_i_j': relabel an image series with two indices, and correct errors from the RDvision transfer program %------------------------------------------------------------------------ -% function GUI_config=relabel_i_j(Param) +% function ParamOut=relabel_i_j(Param) %------------------------------------------------------------------------ @@ -46,9 +46,9 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -function GUI_config=relabel_i_j(Param) +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 ~exist('Param','var') % case with no input parameter - GUI_config={'NbViewMax';1;...% max nbre of input file series (default='' , no limitation) + ParamOut={'NbViewMax';1;...% max nbre of input file series (default='' , no limitation) 'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default) 'WholeIndexRange';'on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) @@ -182,11 +182,11 @@ return end -NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series -if NbSlice~=nbfield_j - answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]); - if ~strcmp(answer,'Yes') - return - end -end +% NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series +% if NbSlice~=nbfield_j +% answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]); +% if ~strcmp(answer,'Yes') +% return +% end +% end %% Set field names and velocity types @@ -209,50 +209,7 @@ end -%% read imadoc -% RootPath=get(hseries.RootPath,'String'); -% RootFile=get(hseries.RootFile,'String'); -% if ~iscell(RootFile) -% msgbox_uvmat('ERROR','please enter an input image series from RDVision system')%error message for xml file reading -% return -% end -% basename=fullfile(RootPath{1},RootFile{1}); -% [XmlData,warntext]=imadoc2struct_special([basename '.xml']);% read the xml file appended to the present function (containing bug corrections) -% if ~isempty(warntext) -% msgbox_uvmat('ERROR',warntext)%error message for xml file reading -% end -% nbfield1=size(XmlData.Time,1); -% nbfield2=size(XmlData.Time,2); -% set(hseries.first_i,'String',num2str(first_label))% display the first image in the process -% set(hseries.last_i,'String',num2str(nbfield1*nbfield2-1+first_label))% display the last image in the process -% set(hseries.nb_field,'String',{num2str(nbfield1*nbfield2-1+first_label)})% display the total nbre of images -% SeriesData=get(hGUI,'UserData'); - - -%% stop program there when it is selected in the menu (no run action) -% if ~exist('num_i1','var') -% return -% end -% if nbfield2>=2 -% answer=msgbox_uvmat('',[num2str(nbfield1) ' bursts containing ' num2str(nbfield2) ' images each']);%error message for directory creation -% nomtype='_i_j'; -% else -% answer=msgbox_uvmat('',['image series with ' num2str(nbfield1) ' images']);%error message for directory creation -% nomtype='_i'; -% end -% if ~strcmp(answer,'Yes') -% return -% end - %% copy and adapt the xml file +NomTypeNew='_1_1'; if ~isempty(XmlData{1}) - -% if exist([basename '.xml'],'file') -% try -% copyfile([basename '.xml'],[basename '.xml~']);% backup the xml file -% catch ME -% msgbox_uvmat('ERROR',ME.message); -% return -% end -% filexml=[filebase{1} '.xml'] t=xmltree(filexml); @@ -267,6 +224,5 @@ j1=j1_series{1}; end - ImageName=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},'_1_1',i1_series{1}(1),[],j); -% ImageName=name_generator(basename,1,1,'.png','_i_j'); + 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']; @@ -282,23 +238,23 @@ %%%% correction RDvision %%%% - if isfield(XmlData,'NbDtj') + if isfield(XmlData{1},'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') + t=set(t,uid_value(1),'value',num2str(XmlData{1}.NbDtj)); + end + end + if isfield(XmlData{1},'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') + t=set(t,uid_value(1),'value',num2str(XmlData{1}.NbDtk)); + end + end + if isempty(j1_series{1}) && isfield(XmlData{1},'NbDti') uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti'); - t=add(t,uid_Dti,'chardata',num2str(XmlData.Dti)); + t=add(t,uid_Dti,'chardata',num2str(XmlData{1}.Dti)); uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti'); - t=add(t,uid_NbDti,'chardata',num2str(XmlData.NbDti)); + t=add(t,uid_NbDti,'chardata',num2str(XmlData{1}.NbDti)); uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); @@ -309,9 +265,9 @@ 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 end @@ -330,6 +286,5 @@ j1=mod(ifile-1+first_label,nbfield2)+1; i1=floor((ifile-1+first_label)/nbfield2)+1; - % filename_new=name_generator(basename,num_i,num_j,'.png',nomtype); - filename_new=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},'_1_1',i1,[],j1); + filename_new=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomTypeNew,i1,[],j1); try movefile(filename,filename_new); @@ -443,7 +398,8 @@ Dtj=[]; s.Dti=Dti; + s.NbDti=NbDti; else % NbDtj=NbDtj/numel(Dtj);%bursts - s.NbDtj=NbDtj; + s.NbDtj=NbDtj/numel(Dtj);%bursts; end %%%% %%%% @@ -456,5 +412,5 @@ end if ~isempty(Dtj) - Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times + 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