[454] | 1 | %'ima_levels': rescale the image intensity to reduce strong luminosity peaks (their blinking effects often perturbs PIV))
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[457] | 2 | % this function can be used as a template for applying a transform (here 'levels.m') to each image of a series
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[171] | 3 | %------------------------------------------------------------------------
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[454] | 4 | % function GUI_input=ima_levels(Param)
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[171] | 5 | %
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[454] | 6 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
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[457] | 7 | %
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| 8 | % This function is used in four modes by the GUI series:
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| 9 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration
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| 10 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops
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| 11 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced.
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| 12 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
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| 13 | %
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[171] | 14 | %OUTPUT
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| 15 | % GUI_input=list of options in the GUI series.fig needed for the function
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| 16 | %
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| 17 | %INPUT:
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[454] | 18 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
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| 19 | % In batch mode, Param is the name of the corresponding xml file containing the same information
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| 20 | % In the absence of input (as activated when the current Action is selected
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| 21 | % in series), the function ouput GUI_input set the activation of the needed GUI elements
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| 22 | %
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| 23 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param)
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| 24 | % .InputTable: cell of input file names, (several lines for multiple input)
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| 25 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
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| 26 | % .OutputSubDir: name of the subdirectory for data outputs
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| 27 | % .OutputDir: directory for data outputs, including path
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| 28 | % .Action: .ActionName: name of the current activated function
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| 29 | % .ActionPath: path of the current activated function
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| 30 | % .IndexRange: set the file or frame indices on which the action must be performed
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| 31 | % .FieldTransform: .TransformName: name of the selected transform function
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| 32 | % .TransformPath: path of the selected transform function
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| 33 | % .TransformHandle: corresponding function handle
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| 34 | % .InputFields: sub structure describing the input fields withfields
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| 35 | % .FieldName: name of the field
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| 36 | % .VelType: velocity type
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| 37 | % .FieldName_1: name of the second field in case of two input series
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| 38 | % .VelType_1: velocity type of the second field in case of two input series
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| 39 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
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| 40 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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| 41 |
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[592] | 42 | function ParamOut=ima_levels (Param)
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[454] | 43 |
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| 44 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName
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[592] | 45 | if isstruct(Param) && isequal(Param.Action.RUN,0)
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| 46 | ParamOut.NbViewMax=1;% max nbre of input file series (default='' , no limitation)
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| 47 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
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| 48 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
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| 49 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
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| 50 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default)
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| 51 | ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
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| 52 | ParamOut.FieldTransform = 'off';%can use a transform function
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| 53 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
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| 54 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default)
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| 55 | ParamOut.OutputDirExt='.lev';%set the output dir extension
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| 56 | return
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[64] | 57 | end
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| 58 |
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[457] | 59 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
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[592] | 60 | %% read input parameters from an xml file if input is a file name (batch mode)
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| 61 | checkrun=1;
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[457] | 62 | if ischar(Param)
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[592] | 63 | Param=xml2struct(Param);% read Param as input file (batch case)
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| 64 | checkrun=0;
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[442] | 65 | end
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[64] | 66 |
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[592] | 67 | ParamOut=Param; %default output
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| 68 | if ~isfield(Param,'InputFields')
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| 69 | Param.InputFields.FieldName='';
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| 70 | end
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| 71 | OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
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| 72 |
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[454] | 73 | %% root input file(s) and type
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| 74 | RootPath=Param.InputTable(:,1);
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| 75 | RootFile=Param.InputTable(:,3);
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| 76 | SubDir=Param.InputTable(:,2);
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| 77 | NomType=Param.InputTable(:,4);
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| 78 | FileExt=Param.InputTable(:,5);
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[551] | 79 | OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
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[454] | 80 |
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[457] | 81 | % get the set of input file names (cell array filecell), and the lists of
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| 82 | % input file or frame indices i1_series,i2_series,j1_series,j2_series
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| 83 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
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| 84 | % filecell{iview,fileindex}: cell array representing the list of file names
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| 85 | % iview: line in the table corresponding to a given file series
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| 86 | % fileindex: file index within the file series,
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| 87 | % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
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| 88 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
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| 89 | % set of frame indices used for movie or multimage input
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[454] | 90 | % numbers of slices and file indices
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[457] | 91 |
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[454] | 92 | NbSlice=1;%default
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| 93 | if isfield(Param.IndexRange,'NbSlice')
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| 94 | NbSlice=Param.IndexRange.NbSlice;
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[442] | 95 | end
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[454] | 96 | nbview=numel(i1_series);%number of input file series (lines in InputTable)
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[457] | 97 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
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| 98 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index
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| 99 | nbfield=nbfield_j*nbfield_i; %total number of fields
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[454] | 100 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices)
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| 101 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
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[442] | 102 |
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[454] | 103 | %determine the file type on each line from the first input file
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| 104 | ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
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[457] | 105 |
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[454] | 106 | [FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1});
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| 107 | CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images
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| 108 | if ~isempty(j1_series{1})
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| 109 | frame_index{1}=j1_series{1};
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| 110 | else
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| 111 | frame_index{1}=i1_series{1};
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[442] | 112 | end
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[454] | 113 |
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| 114 | %% calibration data and timing: read the ImaDoc files
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| 115 | %not relevant for this function
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| 116 |
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| 117 | %% check coincidence in time for several input file series
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| 118 | %not relevant for this function
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| 119 |
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| 120 | %% coordinate transform or other user defined transform
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| 121 | %not relevant for this function
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| 122 |
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| 123 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%%
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| 124 | % EDIT FROM HERE
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| 125 |
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| 126 | %% check the validity of input file types
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| 127 | if CheckImage{1}
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| 128 | FileExtOut='.png'; % write result as .png images for image inputs
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| 129 | if strcmp(lower(NomType{1}(end)),'a')
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| 130 | NomTypeOut=NomType{1};
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| 131 | else
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| 132 | NomTypeOut='_1_1';
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| 133 | end
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| 134 | else
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| 135 | msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image'])
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[128] | 136 | return
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| 137 | end
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[64] | 138 |
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[454] | 139 | %% Set field names and velocity types
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| 140 | %not relevant for this function
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[64] | 141 |
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[454] | 142 | %% Initiate output fields
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| 143 | %not relevant for this function
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| 144 |
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| 145 | %% set processing parameters
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| 146 | % not needed for this function
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| 147 |
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| 148 | %% update the xml file
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| 149 | % not needed for this function
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| 150 |
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| 151 | %% main loop on images
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| 152 | j1=[];%default
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[64] | 153 | for ifile=1:nbfield
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[592] | 154 | if checkrun
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| 155 | stopstate=get(Param.RUNHandle,'BusyAction');
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| 156 | update_waitbar(Param.WaitbarHandle,ifile/nbfield)
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| 157 | else
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| 158 | stopstate='queue';
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| 159 | end
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[64] | 160 | if isequal(stopstate,'queue') % enable STOP command
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[590] | 161 | if ~isempty(j1_series)&&~isequal(j1_series,{[]})
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[454] | 162 | j1=j1_series{1}(ifile);
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[64] | 163 | end
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[454] | 164 | filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
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| 165 | A=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
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| 166 | if ndims(A)==3;%color images
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| 167 | A=sum(double(Aread),3);% take the sum of color components
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| 168 | end
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| 169 | % operation on images
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| 170 | A=levels(A);
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[551] | 171 | filename_new=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
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[454] | 172 | imwrite(A,filename_new)
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| 173 | display([filename_new ' written'])
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[64] | 174 | end
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| 175 | end
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[442] | 176 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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[64] | 177 |
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[454] | 178 |
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[64] | 179 | function C=levels(A)
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| 180 | %whos A;
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| 181 | B=double(A(:,:,1));
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| 182 | windowsize=round(min(size(B,1),size(B,2))/20);
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| 183 | windowsize=floor(windowsize/2)*2+1;
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| 184 | ix=[1/2-windowsize/2:-1/2+windowsize/2];%
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| 185 | %del=np/3;
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| 186 | %fct=exp(-(ix/del).^2);
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| 187 | fct2=cos(ix/(windowsize-1)/2*pi/2);
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| 188 | %Mfiltre=(ones(5,5)/5^2);
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| 189 | %Mfiltre=fct2';
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| 190 | Mfiltre=fct2'*fct2;
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| 191 | Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
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| 192 |
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[71] | 193 | C=filter2(Mfiltre,B);
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[64] | 194 | C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
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| 195 | C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
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| 196 | C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
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| 197 | C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
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| 198 | C=tanh(B./(2*C));
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| 199 | [n,c]=hist(reshape(C,1,[]),100);
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| 200 | % figure;plot(c,n);
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| 201 |
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| 202 | [m,i]=max(n);
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| 203 | c_max=c(i);
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| 204 | [dummy,index]=sort(abs(c-c(i)));
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| 205 | n=n(index);
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| 206 | c=c(index);
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| 207 | i_select = find(cumsum(n)<0.95*sum(n));
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| 208 | if isempty(i_select)
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| 209 | i_select = 1:length(c);
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| 210 | end
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| 211 | c_select=c(i_select);
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| 212 | n_select=n(i_select);
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| 213 | cmin=min(c_select);
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| 214 | cmax=max(c_select);
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| 215 | C=(C-cmin)/(cmax-cmin)*256;
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| 216 | C=uint8(C);
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