Index: /trunk/src/browse_data.m =================================================================== --- /trunk/src/browse_data.m (revision 930) +++ /trunk/src/browse_data.m (revision 931) @@ -47,5 +47,5 @@ %------------------------------------------------------------------------ % --- Executes just before browse_data is made visible. -function browse_data_OpeningFcn(hObject, eventdata, handles, DataSeries,EnableMirror) +function browse_data_OpeningFcn(hObject, eventdata, handles, DataSeries,EnableMirror,MultiDevices) %------------------------------------------------------------------------ @@ -73,4 +73,9 @@ set(hObject, 'Position', FigPos); set(hObject, 'Units', OldUnits); +if exist('MultiDevices','var') && strcmp(MultiDevices,'on') + set(handles.ListDevices,'Max',2) +else + set(handles.ListDevices,'Max',1) +end if exist('EnableMirror','var') && strcmp(EnableMirror,'on') set(handles.CreateMirror,'Visible','on') @@ -608,4 +613,5 @@ Campaign=get(handles.SourceDir,'String'); end +handles.output=[]; handles.output.Campaign=Campaign; Experiment=get(handles.ListExperiments,'String'); Index: /trunk/src/series/extract_multitif.m =================================================================== --- /trunk/src/series/extract_multitif.m (revision 930) +++ /trunk/src/series/extract_multitif.m (revision 931) @@ -142,6 +142,6 @@ ImagesPerLevel=100;%100; count=0; -%count=933;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 67->_11_1 -%count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: +%count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1 +%count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images %% loop on the files for ifile=1:numel(ListFile) @@ -156,8 +156,8 @@ for iframe=1:NbFrames A=imread(ImageName,iframe); - count=count+1; + if isequal(ImagesPerLevel,1)% mode series - OutputFile=fullfile(OutputDir,['img_' num2str(count) '.png']); + OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); else % mode multilevel or volume (indices i and j) i_index=fix(count/ImagesPerLevel)+1; @@ -166,4 +166,5 @@ end imwrite(A,OutputFile,'BitDepth',16) + count=count+1; end end Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 930) +++ /trunk/src/series/extract_rdvision.m (revision 931) @@ -4,5 +4,6 @@ %------------------------------------------------------------------------ % -%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS % +%%%%%%%%%%%%%%%%%%%%%%%%%% % %OUTPUT @@ -243,4 +244,5 @@ + %% reading the .sqb file m = memmapfile(filename_sqb,'Format', { 'uint32' [1 1] 'offset'; ... @@ -286,4 +288,11 @@ 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 + if nbfield2>1 NomTypeNew='_1_1'; @@ -301,8 +310,13 @@ FileDir=SeqData.sequencename; FileDir=regexprep(FileDir,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180' - for i1=1:npi-1 - for j1=1:npj-1 + for i1=1:numel(timestamp)/nbfield2 + for j1=1:nbfield2 OutputFile=fullfile_uvmat(RootPath,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode + try A=imread(OutputFile);% check image reading (stop if error) + catch ME + disp(['checking ' OutputFile]) + disp(ME.message) + end end end @@ -378,5 +392,5 @@ OutputFile=fullfile_uvmat(PathDir,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx)); - if exist(OutputFile,'file') + if exist(OutputFile,'file')% do not recreate existing image file fid=0; else Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 930) +++ /trunk/src/uvmat.m (revision 931) @@ -1273,43 +1273,47 @@ RootPath=read_file_boxes(hhuvmat); -OutPutDir=uigetfile_uvmat('choosean image folder to calibrate with slice position?',fileparts(RootPath),'uigetdir'); -OutPut=browse_data(OutPutDir); +OutPutDir=uigetfile_uvmat('choose an image folder to document with slice position?',fileparts(RootPath),'uigetdir'); +OutPut=browse_data(OutPutDir,'off','on'); nbcalib=0; for ilist=1:numel(OutPut.Experiment) - SubDirBase=regexprep(OutPut.DataSeries{1},'\..+$',''); - XmlFile=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']); - - % read the current xml file - [s,errormsg]=imadoc2struct(XmlFile,'GeometryCalib'); - if ~isempty(errormsg) - msgbox_uvmat('ERROR',['error in reading ' XmlFile ': ' errormsg]) - return - end - GeometryCalib=s.GeometryCalib; - GeometryCalib.NbSlice=SliceData.NbSlice; - GeometryCalib.CheckVolumeScan=SliceData.CheckVolumeScan; - Z_plane=linspace(SliceData.Z(1),SliceData.Z(2),SliceData.NbSlice); - GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; - GeometryCalib.SliceAngle=zeros(GeometryCalib.NbSlice,3); - Angle_1=linspace(SliceData.SliceAngle_1(1),SliceData.SliceAngle_1(2),SliceData.NbSlice); - Angle_2=linspace(SliceData.SliceAngle_2(1),SliceData.SliceAngle_2(2),SliceData.NbSlice); - GeometryCalib.SliceAngle(:,1)=Angle_1';%rotation around x axis (to generalise) - GeometryCalib.SliceAngle(:,2)=Angle_2';%rotation around y axis (to generalise) - GeometryCalib.SliceAngle(:,3)=0; - if SliceData.CheckRefraction - GeometryCalib.InterfaceCoord=[0 0 SliceData.H]; - GeometryCalib.RefractionIndex=SliceData.RefractionIndex; - elseif isfield(GeometryCalib,'RefractionIndex') - GeometryCalib=rmfield(GeometryCalib,'RefractionIndex'); - GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); - end - - % update the current xml file - errormsg=update_imadoc(GeometryCalib,XmlFile,'GeometryCalib');% introduce the calibration data in the xml file - if ~strcmp(errormsg,'') - msgbox_uvmat('ERROR',errormsg); - else - display([XmlFile ' updated with slice positions']) - nbcalib=nbcalib+1; + for idevice=1:numel(OutPut.DataSeries) + SubDirBase=regexprep(OutPut.DataSeries{idevice},'\..+$',''); + XmlFile=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']); + + % read the current xml file + if exist(XmlFile,'file') + [s,errormsg]=imadoc2struct(XmlFile,'GeometryCalib'); + if ~isempty(errormsg) + msgbox_uvmat('ERROR',['error in reading ' XmlFile ': ' errormsg]) + return + end + GeometryCalib=s.GeometryCalib; + GeometryCalib.NbSlice=SliceData.NbSlice; + GeometryCalib.CheckVolumeScan=SliceData.CheckVolumeScan; + Z_plane=linspace(SliceData.Z(1),SliceData.Z(2),SliceData.NbSlice); + GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; + GeometryCalib.SliceAngle=zeros(GeometryCalib.NbSlice,3); + Angle_1=linspace(SliceData.SliceAngle_1(1),SliceData.SliceAngle_1(2),SliceData.NbSlice); + Angle_2=linspace(SliceData.SliceAngle_2(1),SliceData.SliceAngle_2(2),SliceData.NbSlice); + GeometryCalib.SliceAngle(:,1)=Angle_1';%rotation around x axis (to generalise) + GeometryCalib.SliceAngle(:,2)=Angle_2';%rotation around y axis (to generalise) + GeometryCalib.SliceAngle(:,3)=0; + if SliceData.CheckRefraction + GeometryCalib.InterfaceCoord=[0 0 SliceData.H]; + GeometryCalib.RefractionIndex=SliceData.RefractionIndex; + elseif isfield(GeometryCalib,'RefractionIndex') + GeometryCalib=rmfield(GeometryCalib,'RefractionIndex'); + GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); + end + + % update the current xml file + errormsg=update_imadoc(GeometryCalib,XmlFile,'GeometryCalib');% introduce the calibration data in the xml file + if ~strcmp(errormsg,'') + msgbox_uvmat('ERROR',errormsg); + else + display([XmlFile ' updated with slice positions']) + nbcalib=nbcalib+1; + end + end end end