Changeset 1129 for trunk/src/series


Ignore:
Timestamp:
Mar 1, 2024, 8:09:20 PM (5 months ago)
Author:
sommeria
Message:

LIF calibration update and extrct_multitif

Location:
trunk/src/series
Files:
1 added
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/src/series/aver_stat.m

    r1127 r1129  
    298298        for iview=1:NbView
    299299            % reading input file(s)
     300            filecell{iview,index}
    300301            [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
    301302            if ~isempty(errormsg)
     
    469470   
    470471    %% writing the result file
    471     OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
     472    RootPathOut=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
     473    OutputDir=[Param.OutputSubDir Param.OutputDirExt];
     474    OutputFile=fullfile_uvmat(RootPathOut,OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
    472475    if strcmp(FileExtOut,'.png') %case of images
    473476        if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
  • trunk/src/series/extract_multitif.m

    r1127 r1129  
    11%'extract_multitif': read image series from PCO cameras (tiff image series) and write .png images
    2 %------------------------------------------------------------------------
    3    
     2% use a single geometric calibration, with information on the slice positions in case of 3D scanning
     3%------------------------------------------------------
     4% the output file indexing is based on the xml file requested by the
     5% function when it is selected (or possibly inserted in this function in the section TEST)
     6%  This xml file must contain the following information:
     7%   NbDti: the number of 'bursts' -1
     8%   NbDtj: number of frames in each burst-1, or number of repetition of a burst sequence defined by Dtj
     9%   NbDtk: number of repetitions of a slice scanning process -1 (ignored by default)
     10% Therefore the total number of frames is  (NbDti+1)*(NbDtj+1)*(NbDtk+1)
     11% The frame series is stored in a single folder with two indices i:(NbDti+1)*(NbDtk+1)
     12%
     13% To run the function in the cluster in parallel for each multitif file, indicate nb-slice_i equal to the
     14% number input multitif files
     15
     16
    417% function ParamOut=extract_multitif(Param)
    518%
  • trunk/src/series/stereo_input.m

    r1127 r1129  
    243243%show the reference image edit box if relevant (not needed for movies or in the absence of time information
    244244if numel(time)>=2 % if there are at least two time values to define dt
    245     if size(time,1)<MaxIndex_i;
     245    if size(time,1)<MaxIndex_i
    246246        msgbox_uvmat('WARNING','maximum i index restricted by the timing of the xml file');
    247247    elseif size(time,2)<MaxIndex_j
     
    29742974
    29752975% Hint: get(hObject,'Value') returns toggle state of CheckLSM
     2976
     2977
     2978
     2979function num_resolution_Callback(hObject, eventdata, handles)
     2980% hObject    handle to num_resolution (see GCBO)
     2981% eventdata  reserved - to be defined in a future version of MATLAB
     2982% handles    structure with handles and user data (see GUIDATA)
     2983
     2984% Hints: get(hObject,'String') returns contents of num_resolution as text
     2985%        str2double(get(hObject,'String')) returns contents of num_resolution as a double
     2986
     2987
     2988% --- Executes during object creation, after setting all properties.
     2989function num_resolution_CreateFcn(hObject, eventdata, handles)
     2990% hObject    handle to num_resolution (see GCBO)
     2991% eventdata  reserved - to be defined in a future version of MATLAB
     2992% handles    empty - handles not created until after all CreateFcns called
     2993
     2994% Hint: edit controls usually have a white background on Windows.
     2995%       See ISPC and COMPUTER.
     2996if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
     2997    set(hObject,'BackgroundColor','white');
     2998end
  • trunk/src/series/turb_stat.m

    r1127 r1129  
    1 %'aver_stat': calculate Reynolds steress components over time series
     1%'aver_stat': calculate Reynolds stress components over time series
    22%------------------------------------------------------------------------
    33% function ParamOut=turb_stat(Param)
     
    8989RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
    9090WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
    91 
    92 %% define the directory for result file (with path=RootPath{1})
    93 OutputDir=[Param.OutputSubDir Param.OutputDirExt];
    9491   
    9592%% root input file(s) name, type and index series
     
    201198Counter_1=0;
    202199
     200if Param.IndexRange.NbSlice==1
     201    interval=Param.IndexRange.incr_i% statistics is done taking into account the input index increment
     202else
     203    interval=Param.IndexRange.NbSlice;% statistics is done slice by slice without taking into account the input index increment
     204end
     205
    203206%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
    204 % for i_slice=1:Param.IndexRange.NbSlice
    205 %     i_slice
     207for i_slice=1:Param.IndexRange.NbSlice
     208    i_slice
    206209    ind_first=Param.IndexRange.first_i;
    207     for index_i=ind_first:Param.IndexRange.NbSlice:Param.IndexRange.last_i
     210    for index_i=ind_first:interval:Param.IndexRange.last_i
    208211        if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
    209212            disp('program stopped by user')
     
    211214        end
    212215        for index_j=first_j:last_j
    213             InputFile=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},index_i,index_i,index_j,index_j);
    214             [Field,tild,errormsg] = read_field(InputFile,FileType{iview},InputFields{iview});
    215            
    216             %[Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
     216            InputFile=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},index_i,index_i,index_j,index_j)
     217            [Field,tild,errormsg] = read_field(InputFile,FileType{iview},InputFields{iview});       
    217218           
    218219            %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
     
    289290   
    290291    %% writing the result file as netcdf file
    291     OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,ind_first,ind_first,first_j,last_j);
     292    RootPathOut=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
     293    OutputDir=[Param.OutputSubDir Param.OutputDirExt];
     294    OutputFile=fullfile_uvmat(RootPathOut,OutputDir,RootFile{1},FileExtOut,NomTypeOut,ind_first,ind_first,first_j,last_j);
    292295    %case of netcdf input file , determine global attributes
    293296    errormsg=struct2nc(OutputFile,DataOut); %save result file
     
    296299    else
    297300        disp(['error in writting result file: ' errormsg])
    298     end
    299    
    300 % end
     301    end   
     302end
     303
    301304%% open the result file with uvmat (in RUN mode)
    302305if checkrun && isequal(Param.IndexRange.NbSlice,1)
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