Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1202) +++ /trunk/src/series.m (revision 1203) @@ -756,5 +756,5 @@ XmlData=[]; if ~isempty(XmlFileName) - XmlData=read_imadoct(XmlFileName);%read the imadoc file through the local fct read_imadoc + XmlData=read_imadoc(XmlFileName);%read the imadoc file through the local fct read_imadoc if isfield(XmlData,'FileSeries') && Rank==0 set(handles.Relabel,'Visible','on') Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 1202) +++ /trunk/src/series/civ_series.m (revision 1203) @@ -390,48 +390,4 @@ [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B); - - % case of background image to subtract - if par_civ1.CheckBackground &&~isempty(par_civ1.Background) - [RootPath_background,SubDir_background,RootFile_background,~,~,~,~,Ext_background]=fileparts_uvmat(Param.ActionInput.Civ1.Background); - if strcmp(NomTypeNc,'_1-2_1')% case of volume,backgrounds act on different j levels - backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',j1_series_Civ1(ifield)); - elseif isfield(par_civ1,'NbSlice') - i1_background=mod(i1-1,par_civ1.NbSlice)+1; - backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',i1_background); - if strcmp(Param.ActionInput.PairIndices.ListPairMode,'series(Di)')% case of volume, background index refers to j index - par_civ1.NbSlice_j=par_civ1.NbSlice; - end - else - backgroundname=Param.ActionInput.Civ1.Background; - end - if strcmp(backgroundoldname,backgroundname)% background exist, not already read in civ1 - par_civ1.Background=background; %use background already opened - else - if ~isempty(regexp(backgroundname,'(^http://)|(^https://)', 'once'))|| exist(backgroundname,'file') - try - par_civ1.Background=uint16(imread(backgroundname));%update the background, an store it for future use - catch ME - if ~isempty(ME.message) - errormsg=['error reading input image: ' ME.message]; - disp_uvmat('ERROR',errormsg,checkrun) - return - end - end - else - par_civ1.Background=[]; - end - background=par_civ1.Background; - backgroundoldname=backgroundname; - end - par_civ1.ImageA=uint16(par_civ1.ImageA)-par_civ1.Background; - par_civ1.ImageB=uint16(par_civ1.ImageB)-par_civ1.Background; - end - - % case of image luminosity rescaling - if par_civ1.CheckRescale &&~isempty(par_civ1.Maxtanh) - par_civ1.ImageA =par_civ1.Maxtanh*tanh(double(par_civ1.ImageA)/par_civ1.Maxtanh); - par_civ1.ImageB=par_civ1.Maxtanh*tanh(double(par_civ1.ImageB)/par_civ1.Maxtanh); - end - % par_civ1.ImageWidth=size(par_civ1.ImageA,2); % par_civ1.ImageHeight=size(par_civ1.ImageA,1); @@ -467,4 +423,51 @@ Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; Data.CivStage=1; + + + + % case of background image to subtract + if par_civ1.CheckBackground &&~isempty(par_civ1.Background) + [RootPath_background,SubDir_background,RootFile_background,~,~,~,~,Ext_background]=fileparts_uvmat(Param.ActionInput.Civ1.Background); + if strcmp(NomTypeNc,'_1-2_1')% case of volume,backgrounds act on different j levels + backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',j1_series_Civ1(ifield)); + elseif isfield(par_civ1,'NbSlice') + i1_background=mod(i1-1,par_civ1.NbSlice)+1; + backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',i1_background); + if strcmp(Param.ActionInput.PairIndices.ListPairMode,'series(Di)')% case of volume, background index refers to j index + par_civ1.NbSlice_j=par_civ1.NbSlice; + end + else + backgroundname=Param.ActionInput.Civ1.Background; + end + if strcmp(backgroundoldname,backgroundname)% background exist, not already read in civ1 + par_civ1.Background=background; %use background already opened + else + if ~isempty(regexp(backgroundname,'(^http://)|(^https://)', 'once'))|| exist(backgroundname,'file') + try + par_civ1.Background=uint16(imread(backgroundname));%update the background, an store it for future use + catch ME + if ~isempty(ME.message) + errormsg=['error reading input image: ' ME.message]; + disp_uvmat('ERROR',errormsg,checkrun) + return + end + end + else + par_civ1.Background=[]; + end + background=par_civ1.Background; + backgroundoldname=backgroundname; + end + par_civ1.ImageA=uint16(par_civ1.ImageA)-par_civ1.Background; + par_civ1.ImageB=uint16(par_civ1.ImageB)-par_civ1.Background; + end + + % case of image luminosity rescaling + if par_civ1.CheckRescale &&~isempty(par_civ1.Maxtanh) + par_civ1.ImageA =par_civ1.Maxtanh*tanh(double(par_civ1.ImageA)/par_civ1.Maxtanh); + par_civ1.ImageB=par_civ1.Maxtanh*tanh(double(par_civ1.ImageB)/par_civ1.Maxtanh); + end + + % set the list of variables Index: /trunk/src/series/usr_fct/check_field_series.m =================================================================== --- /trunk/src/series/usr_fct/check_field_series.m (revision 1203) +++ /trunk/src/series/usr_fct/check_field_series.m (revision 1203) @@ -0,0 +1,68 @@ +%'check_field_series': checks the existence and type of the input file series +%------------------------------------------------------------------------ +% function GUIParam=check_data_files(Param) +% +%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% +%OUTPUT +% GUISeriesParam=list of 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 +% In the absence of input (as activated when the current Action is selected +% in series), the function ouput GUI_input set the activation of the needed GUI elements + +function GUIParam=check_field_series(Param) + +GUIParam=[]; + +%% input preparation mode (no RUN) +if isstruct(Param) && isequal(Param.Action.RUN,0) + GUIParam.OutputSubDirMode='auto'; %(options 'none'/'custom'/'auto'/'first'/'last','auto' by default) + GUIParam.OutputDirExt='.check_fields';%set the output dir extension + msgbox_uvmat('CONFIMATION','This function will check the series of input fields') + return +end +%------------------------------------------------------------------------ + +%% read input parameters from an xml file if input is a file name (batch mode) +if ischar(Param) + Param=xml2struct(Param);% read Param as input file (batch case) +end + +%% root input file(s) and type +RootPath=Param.InputTable{1,1}; +SubDir=Param.InputTable{1,2}; +RootFile=Param.InputTable{1,3}; +NomType=Param.InputTable{1,4}; +FileExt=Param.InputTable{1,5}; + +%% scans the series indexed with i and j +i_index=Param.IndexRange.first_i:Param.IndexRange.incr_i:Param.IndexRange.last_i; +j_index=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j; +FileCell=cell(numel(j_index),numel(i_index));%initiate cell array of input file names +for ifile=1:numel(i_index) + for jfile=1:numel(j_index) + FullFileName=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i_index(ifile),[],j_index(jfile)); + FileName=fullfile_uvmat('','',RootFile,FileExt,NomType,i_index(ifile),[],j_index(jfile));%name without path + if exist(FullFileName,'file') + FileInfo=get_file_info(FullFileName);% get the info on the file + FileCell{jfile,ifile}=[FileName ': ' FileInfo.FileType]; + else + FileCell{jfile,ifile}=[FileName ': missing']; + end + end +end + +%% transform cell arrays into text and display in workspace +OutputText = strjoin(FileCell, '\n'); %transform cell arrays into text +disp(OutputText) %display the list of files + +%% save the list in the appropriate output folder +OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); +OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; +FullOutputFile=fullfile_uvmat(OutputPath,OutputSubDir,RootFile,'.txt','1-2',i_index(1),i_index(end)) +writelines(OutputText,FullOutputFile); + +'END' +