Jun 13, 2012, 5:04:14 PM (12 years ago)

aver_stat, ima_levels , sub_background now adapted to the new settings
merge_proj, time_series still need to be modified

1 edited


  • trunk/src/series/ima_levels.m

    r447 r454  
    1 %'ima_levels': rescale the image intensity to reduce strong luminosity peaks
     1%'ima_levels': rescale the image intensity to reduce strong luminosity peaks (their blinking effects often perturbs PIV))
     2% this function can be used as a template for applying a transform (here 'levels.m') on each image of a series
    3 % function GUI_input=ima_levels(num_i1,num_i2,num_j1,num_j2,Series)
     4% function GUI_input=ima_levels(Param)
     6%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
    68% GUI_input=list of options in the GUI series.fig needed for the function
    9 %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    10 %num_i2:  series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
    11 %num_j1:  series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
    12 %num_j2:  series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
    13 %Series: Matlab structure containing information set by the series interface% relabel_i_j: relabel an image series with two indices, according to the time matrix given by ImaDoc
    14 %----------------------------------------------------------------------
    15 function GUI_input=ima_levels(Param)
    16 %requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
    17 if ~exist('Param','var')
    18     GUI_input={'OutputDirExt';'.lev'};
    19     return %exit the function
     11% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
     12% In batch mode, Param is the name of the corresponding xml file containing the same information
     13% In the absence of input (as activated when the current Action is selected
     14% in series), the function ouput GUI_input set the activation of the needed GUI elements
     16% Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param)
     17%    .InputTable: cell of input file names, (several lines for multiple input)
     18%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
     19%    .OutputSubDir: name of the subdirectory for data outputs
     20%    .OutputDir: directory for data outputs, including path
     21%    .Action: .ActionName: name of the current activated function
     22%             .ActionPath:   path of the current activated function
     23%    .IndexRange: set the file or frame indices on which the action must be performed
     24%    .FieldTransform: .TransformName: name of the selected transform function
     25%                     .TransformPath:   path  of the selected transform function
     26%                     .TransformHandle: corresponding function handle
     27%    .InputFields: sub structure describing the input fields withfields
     28%              .FieldName: name of the field
     29%              .VelType: velocity type
     30%              .FieldName_1: name of the second field in case of two input series
     31%              .VelType_1: velocity type of the second field in case of two input series
     32%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
     35function GUI_input=ima_levels (Param)
     37%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
     38if ~exist('Param','var') % case with no input parameter
     39    GUI_input={'NbViewMax';1;...% max nbre of input file series (default='' , no limitation)
     40        'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default)
     41        'NbSlice';'off'; ...%nbre of slices ('off' by default)
     42        'VelType';'off';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
     43        'FieldName';'off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
     44        'FieldTransform'; 'off';...%can use a transform function
     45        'ProjObject';'off';...%can use projection object(option 'off'/'on',
     46        'Mask';'off';...%can use mask option   (option 'off'/'on', 'off' by default)
     47        'OutputDirExt';'.lev';...%set the output dir extension
     48               ''};
     49        return
    22 %% input parameters
    23 % read the xml file for batch case
    24 if ischar(Param) && ~isempty(find(regexp('Param','.xml$')))
     52%% get input parameters, file names and indices
     53% BATCH  case: read the xml file for batch case
     54if ischar(Param) && ~isempty(find(regexp(Param,'.xml$')))
    2555    Param=xml2struct(Param);
    2656    checkrun=0;
    27 else %  RUN case: parameters introduced as the input structure Param
     57% RUN case: parameters introduced as the input structure Param 
    2859    hseries=guidata(Param.hseries);%handles of the GUI series
    29     WaitbarPos=get(hseries.waitbar_frame,'Position');
    30     checkrun=1;
     60    WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series
     61    checkrun=1; % indicate the RUN option is used
    32 %filebase=fullfile(Param.InputTable{1,1},Param.InputTable{1,3});
    33 RootPath=Param.InputTable{1,1};
    34 Subdir=Param.InputTable{1,2};
    35 RootFile=Param.InputTable{1,3};
    36 NomType=Param.InputTable{1,4};
    37 FileExt=Param.InputTable{1,5};
    38 [filecell,i1_series,i2_series,j1_series]=get_file_series(Param);% list of input files and indices
    39 if size(filecell,1)>1
    40     msgbox_uvmat('WARNING','This function uses only the first input image series')
     64% get the set of input file names (cell array filecell), and the lists of
     67%% root input file(s) and type
     74% numbers of slices and file indices
     76if isfield(Param.IndexRange,'NbSlice')
     77    NbSlice=Param.IndexRange.NbSlice;
     79nbview=numel(i1_series);%number of input file series (lines in InputTable)
     80nbfield_j=size(i1_series{1},1); %nb of consecutive fields for the j index (bursts or volume slices)
     81nbfield_i=size(i1_series{1},2); %nb of consecutive fields for the i index
     82nbfield=nbfield_j*nbfield_i; %total number of files or frames
     83nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
     84nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
     86%determine the file type on each line from the first input file
     87ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
     89CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images
     90if ~isempty(j1_series{1})
     91    frame_index{1}=j1_series{1};
     93    frame_index{1}=i1_series{1};
     96%% calibration data and timing: read the ImaDoc files
     97%not relevant for this function
     99%% check coincidence in time for several input file series
     100%not relevant for this function
     102%% coordinate transform or other user defined transform
     103%not relevant for this function
     105%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
     106 % EDIT FROM HERE
     108 %% check the validity of  input file types
     109if CheckImage{1}
     110    FileExtOut='.png'; % write result as .png images for image inputs
     111    if strcmp(lower(NomType{1}(end)),'a')
     112        NomTypeOut=NomType{1};
     113    else
     114        NomTypeOut='_1_1';
     115    end
     117    msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image'])
    41118    return
    44 %% determine input image type
    45 [FileType,FileInfo,MovieObject]=get_file_type(filecell{1,1});
    46 ListTypes={'image','multimage','mmreader','video'};
     121%% Set field names and velocity types
     122%not relevant for this function
    48 if isempty(strcmp(FileType,ListTypes))% if the detected FileType is not in the list for images
    49     msgbox_uvmat('ERROR',['invalid file extension ' FileExt ': this function only accepts image or movie input'])
    50     return
    51 end
     124%% Initiate output fields
     125%not relevant for this function
    53 %% create dir of the new images
    54 SubdirResult=[Param.InputTable{1,2} '.lev'];% add the suffix '.lev' to the name of the image folder
    55 try
    56     mkdir(fullfile(Param.InputTable{1,1},SubdirResult));
    57 catch ME
    58     msgbox_uvmat('ERROR',['error in creating result directory: ' ME.message]);%display error msg for directory creation if fails
    59     return
    60 end
    61 [xx,msg2] = fileattrib(fullfile(Param.InputTable{1,1},SubdirResult),'+w','g'); %yield writing access (+w) to user group (g)
    62 if ~strcmp(msg2,'')
    63     msgbox_uvmat('ERROR',['pb of permission for ' fullfile(Param.InputTable{1,1},SubdirResult) ': ' msg2])%error message for directory creation
    64     return
    65 end
    66 msgbox_uvmat('CONFIRMATION','apply image rescaling function levels.m ');
     127%% set processing parameters
     128% not needed for this function
    68 %copy the xml file
    69 % if exist([basename '.xml'],'file')
    70 %     copyfile([basename '.xml'],[basename_new '.xml']);% copy the .civ file
    71 % end
     130%% update the xml file
     131% not needed for this function
    73 %% main loop
    74 nbfield=size(i1_series{1},2);
    75 nbfield2=size(i1_series{1},1);
     133%% main loop on images
    76135for ifile=1:nbfield
    77136    if checkrun
    78 %         update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield)
    79137        update_waitbar(hseries.waitbar_frame,WaitbarPos,ifile/nbfield)
    80138        stopstate=get(hseries.RUN,'BusyAction');
    83141    end
    84142    if isequal(stopstate,'queue') % enable STOP command
    85         for jfile=1:nbfield2
    86             %filename=name_generator(basename,num_i1(jfile,ifile),num_j1(jfile,ifile),Series.FileExt,Series.NomType);
    87             %filename_new=name_generator(basename_new,num_i1(jfile,ifile),num_j1(jfile,ifile),'.png',Series.NomType);
    88             filename=fullfile_uvmat(RootPath,Subdir,RootFile,FileExt,NomType,i1_series{1}(jfile,ifile),[],j1_series{1}(jfile,ifile));
    89             switch FileType
    90                 case {'video','mmreader'}
    91                     A=read(MovieObject,i1_series{1}(jfile,ifile));
    92                     if strcmp(NomType,'*')
    93                         A=read(MovieObject,i1_series{1}(jfile,ifile));
    94                         NomType_out='_1';
    95                     else
    96                         A=imread(filename,j1_series{1}(jfile,ifile));
    97                         NomType_out='_1_1';
    98                     end
    99                 case {'vol','image'}
    100                     A=imread(filename);
    101                     NomType_out='_1';
    102                 case 'multimage'
    103                     if strcmp(NomType,'*')
    104                         A=imread(filename,i1_series{1}(jfile,ifile));
    105                         NomType_out='_1';
    106                     else
    107                         A=imread(filename,j1_series{1}(jfile,ifile));
    108                         NomType_out='_1_1';
    109                     end
    110             end
    111             C=levels(A);
    112             filename_new=fullfile_uvmat(RootPath,SubdirResult,RootFile,'.png',NomType_out,i1_series{1}(jfile,ifile),[],j1_series{1}(jfile,ifile));
    113             imwrite(C,filename_new)
    114             display([filename_new ' written'])
     143        if ~isempty(j1_series)
     144            j1=j1_series{1}(ifile);
    115145        end
     146        filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
     147        A=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
     148        if ndims(A)==3;%color images
     149            A=sum(double(Aread),3);% take the sum of color components
     150        end
     151        % operation on images
     152        A=levels(A);
     153        filename_new=fullfile_uvmat(RootPath{1},Param.OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
     154        imwrite(A,filename_new)
     155        display([filename_new ' written'])
    116156    end
    120161function C=levels(A)
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