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