[457] | 1 | %'sub_background': substract a sliding background to an image series |
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[169] | 2 | %------------------------------------------------------------------------ |
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[24] | 3 | % Method: |
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| 4 | %calculate the background image by sorting the luminosity of each point |
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| 5 | % over a sliding sub-sequence of 'nbaver_ima' images. |
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| 6 | % The luminosity value of rank 'rank' is selected as the |
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| 7 | % 'background'. rank=nbimages/2 gives the median value. Smaller values are appropriate |
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| 8 | % for a dense set of particles. The extrem value rank=1 gives the true minimum |
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| 9 | % luminosity, but it can be polluted by noise. |
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| 10 | % Organization of image indices: |
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[454] | 11 | % The program is working on a series of images, |
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| 12 | % The processing can be done over groups of nbfield2 consecutive files in slices (parameter NbSlice) |
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| 13 | % In the mode 'volume', nbfield2=1 (1 image at each level)and NbSlice (=nbfield_j) |
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| 14 | % Else nbfield2=nbfield_j =nbre of images in a burst (j index) |
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[451] | 15 | |
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[457] | 16 | % function GUI_config=sub_background(Param) |
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[169] | 17 | % |
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[451] | 18 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[457] | 19 | % |
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| 20 | % This function is used in four modes by the GUI series: |
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| 21 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 22 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 23 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 24 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 25 | % |
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[451] | 26 | %OUTPUT |
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[454] | 27 | % GUI_series_config=list of options in the GUI series.fig needed for the function |
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[451] | 28 | % |
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| 29 | %INPUT: |
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| 30 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 31 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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| 32 | % In the absence of input (as activated when the current Action is selected |
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[454] | 33 | % in series), the function ouput GUI_series_config set the activation of the needed GUI elements |
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[451] | 34 | % |
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| 35 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
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| 36 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 37 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 38 | % .OutputSubDir: name of the subdirectory for data outputs |
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[474] | 39 | % .OutputDirExt: extension for the directory for data outputs |
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[451] | 40 | % .Action: .ActionName: name of the current activated function |
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| 41 | % .ActionPath: path of the current activated function |
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| 42 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 43 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 44 | % .TransformPath: path of the selected transform function |
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| 45 | % .TransformHandle: corresponding function handle |
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| 46 | % .InputFields: sub structure describing the input fields withfields |
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| 47 | % .FieldName: name of the field |
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| 48 | % .VelType: velocity type |
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| 49 | % .FieldName_1: name of the second field in case of two input series |
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| 50 | % .VelType_1: velocity type of the second field in case of two input series |
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| 51 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 52 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 53 | |
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| 54 | |
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[459] | 55 | function ParamOut=sub_background (Param) |
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[24] | 56 | |
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[592] | 57 | %% input preparation mode (no RUN) |
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| 58 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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| 59 | ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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| 60 | ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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| 61 | ParamOut.NbSlice='on'; ...%nbre of slices ('off' by default) |
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| 62 | ParamOut.VelType='off';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 63 | ParamOut.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 64 | ParamOut.FieldTransform = 'off';...%can use a transform function |
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| 65 | ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on', |
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| 66 | ParamOut.Mask='off';...%can use mask option (option 'off'/'on', 'off' by default) |
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| 67 | ParamOut.OutputDirExt='.sback';%set the output dir extension |
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| 68 | |
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| 69 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 70 | |
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| 71 | %% root input file(s) and type |
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| 72 | % RootPath=Param.InputTable(:,1); |
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| 73 | % RootFile=Param.InputTable(:,3); |
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| 74 | % SubDir=Param.InputTable(:,2); |
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| 75 | % NomType=Param.InputTable(:,4); |
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| 76 | % FileExt=Param.InputTable(:,5); |
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| 77 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 78 | %%%%%%%%%%%% |
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| 79 | % The cell array filecell is the list of input file names, while |
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| 80 | % filecell{iview,fileindex}: |
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| 81 | % iview: line in the table corresponding to a given file series |
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| 82 | % fileindex: file index within the file series, |
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| 83 | % 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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| 84 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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| 85 | %%%%%%%%%%%% |
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| 86 | NbSlice=1;%default |
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| 87 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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| 88 | NbSlice=Param.IndexRange.NbSlice; |
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| 89 | end |
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| 90 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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| 91 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 92 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 93 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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| 94 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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| 95 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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| 96 | |
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| 97 | %determine the file type on each line from the first input file |
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| 98 | |
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| 99 | |
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| 100 | %% calibration data and timing: read the ImaDoc files |
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| 101 | %not relevant here |
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| 102 | |
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| 103 | %% check coincidence in time for several input file series |
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| 104 | %not relevant here |
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| 105 | |
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| 106 | %% coordinate transform or other user defined transform |
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| 107 | %not relevant here |
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| 108 | |
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| 109 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 110 | % EDIT FROM HERE |
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| 111 | |
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| 112 | %% check the validity of input file types |
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| 113 | ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images) |
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| 114 | FileType=get_file_type(filecell{1,1}); |
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| 115 | CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions), 1));% =1 for images |
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| 116 | if ~CheckImage |
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| 117 | msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image']) |
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[451] | 118 | return |
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[592] | 119 | end |
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| 120 | |
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| 121 | %% Set field names and velocity types |
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| 122 | %not relevant here |
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| 123 | |
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| 124 | %% Initiate output fields |
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| 125 | %not relevant here |
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| 126 | |
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| 127 | %%% SPECIFIC PART BEGINS HERE |
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| 128 | NbSlice=1; |
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| 129 | if isfield(Param.IndexRange,'NbSlice') |
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| 130 | NbSlice=Param.IndexRange.NbSlice; %number of slices |
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| 131 | end |
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| 132 | %siz=size(i1_series); |
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| 133 | nbaver_init=23;%approximate number of images used for the sliding background: to be adjusted later to include an integer number of bursts |
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| 134 | j1=[];%default |
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| 135 | |
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| 136 | %% adjust the proposed number of images in the sliding average to include an integer number of bursts |
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| 137 | if nbfield_i~=1 |
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| 138 | nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background, |
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| 139 | if isequal(floor(nbaver/2),nbaver) |
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| 140 | nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined) |
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| 141 | end |
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| 142 | nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts |
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| 143 | end |
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| 144 | |
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| 145 | %% input of specific parameters |
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| 146 | %if checkrun %get specific parameters interactively |
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| 147 | if isequal(Param.Action.RUN,0) |
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| 148 | prompt = {'volume scan mode (Yes/No)';'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';... |
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| 149 | 'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'}; |
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| 150 | dlg_title = 'get (slice by slice) a sliding background and substract to each image'; |
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| 151 | num_lines= 3; |
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| 152 | def = { 'No';num2str(nbaver_init);'0.1'}; |
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| 153 | answer = inputdlg(prompt,dlg_title,num_lines,def); |
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| 154 | |
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| 155 | %check input consistency |
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| 156 | if strcmp(answer{1},'No') && ~isequal(NbSlice,1) |
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| 157 | check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice) ' slices']); |
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| 158 | if ~strcmp(check,'Yes') |
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| 159 | return |
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| 160 | end |
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| 161 | end |
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| 162 | if strcmp(answer{1},'Yes') |
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| 163 | step=1; |
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| 164 | else |
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| 165 | step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst |
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| 166 | end |
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| 167 | nbaver_ima=str2num(answer{2});%number of images for the sliding background |
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| 168 | nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background |
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| 169 | if isequal(floor(nbaver/2),nbaver) |
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| 170 | nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) |
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| 171 | end |
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| 172 | nbaver_ima=nbaver*step; |
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| 173 | end |
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| 174 | ParamOut.InputGUI.CheckVolume=strcmp(answer{1},'Yes'); |
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| 175 | ParamOut.InputGUI.SlidingSequenceLength=nbaver_ima; |
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| 176 | ParamOut.InputGUI.BrightnessRankThreshold=str2num(answer{3}); |
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| 177 | |
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| 178 | % apply the image rescaling function 'level' (avoid the blinking effects of bright particles) |
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| 179 | answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background'); |
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| 180 | ParamOut.InputGUI.CheckLevelTransform=strcmp(answer,'Yes'); |
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| 181 | return |
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[24] | 182 | end |
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[592] | 183 | %%%%%%%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[24] | 184 | |
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[592] | 185 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 186 | checkrun=1; |
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[457] | 187 | if ischar(Param) |
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[592] | 188 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 189 | checkrun=0; |
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[374] | 190 | end |
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[457] | 191 | |
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[592] | 192 | %% Input preparation |
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| 193 | nbaver_ima=Param.InputGUI.SlidingSequenceLength; |
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| 194 | NbSlice=Param.IndexRange.NbSlice; |
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| 195 | if ~isequal(NbSlice,1) |
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| 196 | display(['multi-level splitting into ' num2str(NbSlice) ' slices']); |
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| 197 | end |
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[457] | 198 | RootPath=Param.InputTable(:,1); |
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| 199 | RootFile=Param.InputTable(:,3); |
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| 200 | SubDir=Param.InputTable(:,2); |
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| 201 | NomType=Param.InputTable(:,4); |
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| 202 | FileExt=Param.InputTable(:,5); |
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[451] | 203 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[592] | 204 | [FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); |
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| 205 | if ~isempty(j1_series{1}) |
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| 206 | frame_index{1}=j1_series{1}; |
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| 207 | else |
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| 208 | frame_index{1}=i1_series{1}; |
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| 209 | end |
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[454] | 210 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 211 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 212 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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[592] | 213 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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[454] | 214 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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[451] | 215 | |
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[592] | 216 | %% Output |
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| 217 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 218 | if strcmp(lower(NomType{1}(end)),'a') |
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| 219 | NomTypeOut=NomType{1};%case of letter appendix |
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| 220 | elseif isempty(j1_series) |
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| 221 | NomTypeOut='_1'; |
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[454] | 222 | else |
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[592] | 223 | NomTypeOut='_1_1';% caseof purely numerical indexing |
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[454] | 224 | end |
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[451] | 225 | |
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[592] | 226 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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[451] | 227 | |
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[592] | 228 | if isequal(Param.InputGUI.CheckVolume,1) |
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| 229 | step=1; |
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| 230 | else |
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| 231 | step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst |
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[54] | 232 | end |
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[592] | 233 | nbaver_ima=Param.InputGUI.SlidingSequenceLength;%number of images for the sliding background |
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| 234 | nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background |
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| 235 | if isequal(floor(nbaver/2),nbaver) |
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| 236 | nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) |
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[24] | 237 | end |
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[592] | 238 | nbaver_ima=nbaver*step; |
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| 239 | if nbaver_ima > nbfield |
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| 240 | display('number of images in a slice smaller than the proposed number of images for the sliding average') |
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| 241 | return |
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[24] | 242 | end |
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[454] | 243 | |
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| 244 | % calculate absolute brightness rank |
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[592] | 245 | rank=floor(Param.InputGUI.BrightnessRankThreshold*nbaver_ima); |
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[24] | 246 | if rank==0 |
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| 247 | rank=1;%rank selected in the sorted image series |
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| 248 | end |
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| 249 | |
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[239] | 250 | %% prealocate memory for the sliding background |
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[394] | 251 | try |
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[454] | 252 | Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1)); |
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| 253 | [npy,npx]=size(Afirst); |
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| 254 | if strcmp(class(Afirst),'uint8') % case of 8bit images |
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| 255 | Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory |
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| 256 | Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory |
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| 257 | else |
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| 258 | Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
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| 259 | Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
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| 260 | end |
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[239] | 261 | catch ME |
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[592] | 262 | msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message]) |
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[239] | 263 | return |
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| 264 | end |
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| 265 | |
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[442] | 266 | %% update the xml file |
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[454] | 267 | % SubDirBase=regexprep(Param.InputTable{1,2},'\..*','');%take the root part of SubDir, before the first dot '.' |
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| 268 | % filexml=fullfile(RootPath{1},[SubDirBase '.xml']); |
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| 269 | % if ~exist(filexml,'file') && exist([fullfile(RootPath{1},SubDir{1},RootFile{1}) '.xml'],'file')% xml inside the image directory |
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| 270 | % copyfile([filebase '.xml'],filexml);% copy the .xml file |
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| 271 | % end |
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| 272 | % if exist(filexml,'file') |
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| 273 | % t=xmltree(filexml); |
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| 274 | % %update information on the first image name in the series |
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| 275 | % uid_Heading=find(t,'ImaDoc/Heading'); |
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| 276 | % if isempty(uid_Heading) |
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| 277 | % [t,uid_Heading]=add(t,1,'element','Heading'); |
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| 278 | % end |
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| 279 | % uid_ImageName=find(t,'ImaDoc/Heading/ImageName'); |
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| 280 | % if ~isempty(j1_series{1}) |
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| 281 | % j1=j1_series{1}(1); |
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| 282 | % end |
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| 283 | % ImageName=fullfile_uvmat([dir_images term],'',RootFile{1},'.png',NomType,i1_series(1,1),[],j1); |
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| 284 | % [pth,ImageName]=fileparts(ImageName); |
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| 285 | % ImageName=[ImageName '.png']; |
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| 286 | % if isempty(uid_ImageName) |
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| 287 | % [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); |
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| 288 | % end |
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| 289 | % uid_value=children(t,uid_ImageName); |
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| 290 | % if isempty(uid_value) |
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| 291 | % t=add(t,uid_ImageName,'chardata',ImageName);%indicate name of the first image, with ;png extension |
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| 292 | % else |
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| 293 | % t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension |
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| 294 | % end |
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| 295 | % |
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| 296 | % %add information about image transform |
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| 297 | % [t,new_uid]=add(t,1,'element','ImageTransform'); |
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| 298 | % [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction'); |
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| 299 | % [t]=add(t,NameFunction_uid,'chardata','sub_background'); |
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| 300 | % if GUI_config.CheckLevel |
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| 301 | % [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction'); |
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| 302 | % [t]=add(t,NameFunction_uid,'chardata','levels'); |
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| 303 | % end |
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| 304 | % [t,NbSlice_uid]=add(t,new_uid,'element','NbSlice'); |
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| 305 | % [t]=add(t,new_uid,'chardata',num2str(NbSlice)); |
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| 306 | % [t,NbSlidingImages_uid]=add(t,new_uid,'element','NbSlidingImages'); |
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| 307 | % [t]=add(t,NbSlidingImages_uid,'chardata',num2str(nbaver)); |
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| 308 | % [t,LuminosityRank_uid]=add(t,new_uid,'element','RankBackground'); |
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| 309 | % [t]=add(t,LuminosityRank_uid,'chardata',num2str(rank));% luminosity rank almong the nbaver sliding images |
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| 310 | % save(t,filexml) |
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| 311 | % end |
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[24] | 312 | %copy the mask |
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[442] | 313 | % if exist([filebase '_1mask_1'],'file') |
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| 314 | % copyfile([filebase '_1mask_1'],[filebase_b '_1mask_1']);% copy the mask file |
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| 315 | % end |
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[24] | 316 | |
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| 317 | %MAIN LOOP ON SLICES |
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[451] | 318 | for islice=1:NbSlice |
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[214] | 319 | %% select the series of image indices at the level islice |
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[454] | 320 | indselect=islice:NbSlice*step:nbfield;% select file indices of the slice |
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| 321 | for ifield=1:step-1 |
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| 322 | indselect=[indselect;indselect(end,:)+1]; |
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[394] | 323 | end |
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[214] | 324 | |
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| 325 | %% read the first series of nbaver_ima images and sort by luminosity at each pixel |
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[24] | 326 | for ifield = 1:nbaver_ima |
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[54] | 327 | ifile=indselect(ifield); |
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[394] | 328 | filename=filecell{1,ifile}; |
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[454] | 329 | Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); |
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| 330 | if ndims(Aread)==3;%color images |
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| 331 | Aread=sum(double(Aread),3);% take the sum of color components |
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| 332 | end |
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[394] | 333 | Ak(:,:,ifield)=Aread; |
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[24] | 334 | end |
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| 335 | Asort=sort(Ak,3);%sort the luminosity of images at each point |
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| 336 | B=Asort(:,:,rank);%background image |
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[394] | 337 | display( 'first background image will be substracted') |
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[454] | 338 | nbfirst=(ceil(nbaver/2))*step; |
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[24] | 339 | for ifield=1:nbfirst |
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[394] | 340 | Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image |
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| 341 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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| 342 | ifile=indselect(ifield); |
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| 343 | if ~isempty(j1_series{1}) |
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| 344 | j1=j1_series{1}(ifile); |
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| 345 | end |
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[474] | 346 | newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
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[454] | 347 | |
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| 348 | %write result file |
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[592] | 349 | if Param.InputGUI.CheckLevelTransform |
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[454] | 350 | C=levels(Acor); |
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[394] | 351 | imwrite(C,newname,'BitDepth',8); % save the new image |
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| 352 | else |
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[454] | 353 | if isequal(FileInfo{1}.BitDepth,16) |
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| 354 | C=uint16(Acor); |
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| 355 | imwrite(C,newname,'BitDepth',16); % save the new image |
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| 356 | else |
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| 357 | C=uint8(Acor); |
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| 358 | imwrite(C,newname,'BitDepth',8); % save the new image |
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| 359 | end |
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[394] | 360 | end |
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[454] | 361 | display([newname ' written']) |
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[24] | 362 | end |
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[214] | 363 | |
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[454] | 364 | %% repeat the operation on a sliding series of images |
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[214] | 365 | display('sliding background image will be substracted') |
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[454] | 366 | if nbfield_i > nbaver_ima |
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| 367 | for ifield = step*ceil(nbaver/2)+1:step:nbfield_i-step*floor(nbaver/2) |
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[442] | 368 | if checkrun |
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[592] | 369 | stopstate=get(Param.RUNHandle,'BusyAction'); |
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| 370 | update_waitbar(Param.WaitbarHandle,(ifield+(islice-1)*nbfield_i)/(nbfield_i*NbSlice)) |
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[442] | 371 | else |
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| 372 | stopstate='queue'; |
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| 373 | end |
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| 374 | if isequal(stopstate,'queue')% enable STOP command |
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[240] | 375 | Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step) |
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[24] | 376 | %incorporate next burst in the current image series |
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| 377 | for iburst=1:step |
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| 378 | ifile=indselect(ifield+step*floor(nbaver/2)+iburst-1); |
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[454] | 379 | filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1_series{1}(ifile)); |
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| 380 | Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile)); |
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| 381 | if ndims(Aread)==3;%color images |
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| 382 | Aread=sum(double(Aread),3);% take the sum of color components |
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| 383 | end |
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[24] | 384 | Ak(:,:,nbaver_ima-step+iburst)=Aread; |
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| 385 | end |
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| 386 | Asort=sort(Ak,3);%sort the new current image series by luminosity |
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| 387 | B=Asort(:,:,rank);%current background image |
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| 388 | for iburst=1:step |
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| 389 | index=step*floor(nbaver/2)+iburst; |
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| 390 | Acor=double(Ak(:,:,index))-double(B); |
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| 391 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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| 392 | ifile=indselect(ifield+iburst-1); |
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[394] | 393 | if ~isempty(j1_series{1}) |
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| 394 | j1=j1_series{1}(ifile); |
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| 395 | end |
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[474] | 396 | newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
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[454] | 397 | %write result file |
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[592] | 398 | if Param.InputGUI.CheckLevelTransform |
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[454] | 399 | C=levels(Acor); |
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[214] | 400 | imwrite(C,newname,'BitDepth',8); % save the new image |
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| 401 | else |
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[454] | 402 | if isequal(FileInfo{1}.BitDepth,16) |
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| 403 | C=uint16(Acor); |
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| 404 | imwrite(C,newname,'BitDepth',16); % save the new image |
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| 405 | else |
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| 406 | C=uint8(Acor); |
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| 407 | imwrite(C,newname,'BitDepth',8); % save the new image |
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| 408 | end |
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[214] | 409 | end |
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[454] | 410 | display([newname ' written']) |
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| 411 | |
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[214] | 412 | end |
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[24] | 413 | else |
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| 414 | return |
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| 415 | end |
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| 416 | end |
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| 417 | end |
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[394] | 418 | |
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| 419 | %% substract the background from the last images |
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[214] | 420 | display('last background image will be substracted') |
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[454] | 421 | ifield=nbfield_i-(step*ceil(nbaver/2))+1:nbfield_i; |
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| 422 | for ifield=nbfield_i-(step*floor(nbaver/2))+1:nbfield_i |
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| 423 | index=ifield-nbfield_i+step*(2*floor(nbaver/2)+1); |
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[394] | 424 | Acor=double(Ak(:,:,index))-double(B); |
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| 425 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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| 426 | ifile=indselect(ifield); |
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| 427 | if ~isempty(j1_series{1}) |
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| 428 | j1=j1_series{1}(ifile); |
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| 429 | end |
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[474] | 430 | newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
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[454] | 431 | |
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| 432 | %write result file |
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[592] | 433 | if Param.InputGUI.CheckLevelTransform |
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[454] | 434 | C=levels(Acor); |
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[394] | 435 | imwrite(C,newname,'BitDepth',8); % save the new image |
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| 436 | else |
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[454] | 437 | if isequal(FileInfo{1}.BitDepth,16) |
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| 438 | C=uint16(Acor); |
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| 439 | imwrite(C,newname,'BitDepth',16); % save the new image |
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| 440 | else |
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| 441 | C=uint8(Acor); |
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| 442 | imwrite(C,newname,'BitDepth',8); % save the new image |
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| 443 | end |
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[394] | 444 | end |
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[454] | 445 | display([newname ' written']) |
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[394] | 446 | end |
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[24] | 447 | end |
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| 448 | |
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[214] | 449 | |
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| 450 | function C=levels(A) |
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| 451 | %whos A; |
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| 452 | B=double(A(:,:,1)); |
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| 453 | windowsize=round(min(size(B,1),size(B,2))/20); |
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| 454 | windowsize=floor(windowsize/2)*2+1; |
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[239] | 455 | ix=1/2-windowsize/2:-1/2+windowsize/2;% |
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[214] | 456 | %del=np/3; |
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| 457 | %fct=exp(-(ix/del).^2); |
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| 458 | fct2=cos(ix/(windowsize-1)/2*pi/2); |
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| 459 | %Mfiltre=(ones(5,5)/5^2); |
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| 460 | %Mfiltre=fct2'; |
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| 461 | Mfiltre=fct2'*fct2; |
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| 462 | Mfiltre=Mfiltre/(sum(sum(Mfiltre))); |
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| 463 | |
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| 464 | C=filter2(Mfiltre,B); |
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| 465 | C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize); |
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| 466 | C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize); |
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| 467 | C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:); |
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| 468 | C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:); |
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| 469 | C=tanh(B./(2*C)); |
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| 470 | [n,c]=hist(reshape(C,1,[]),100); |
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| 471 | % figure;plot(c,n); |
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| 472 | |
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| 473 | [m,i]=max(n); |
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| 474 | c_max=c(i); |
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| 475 | [dummy,index]=sort(abs(c-c(i))); |
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| 476 | n=n(index); |
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| 477 | c=c(index); |
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| 478 | i_select = find(cumsum(n)<0.95*sum(n)); |
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| 479 | if isempty(i_select) |
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| 480 | i_select = 1:length(c); |
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| 481 | end |
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| 482 | c_select=c(i_select); |
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| 483 | n_select=n(i_select); |
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| 484 | cmin=min(c_select); |
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| 485 | cmax=max(c_select); |
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| 486 | C=(C-cmin)/(cmax-cmin)*256; |
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| 487 | C=uint8(C); |
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