[169] | 1 | %'sub_background': substract background to an image series, used with series.fig |
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| 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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| 11 | % The program is working on a series of images, labelled by two indices i and j, given |
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| 12 | % by the input matlab vectors num_i1 and num_j1 respectively. In the list, j is the fastest increasing index. |
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| 13 | % The processing can be done in slices (number nbslice), with bursts of |
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| 14 | % nbfield2 successive images for a given slice (mode 'multilevel') |
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[169] | 15 | % In the mode 'volume', nbfield2=1 (1 image at each level) |
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[451] | 16 | |
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| 17 | % function GUI_input=sub_background(Param) |
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[169] | 18 | % |
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[451] | 19 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 20 | %OUTPUT |
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| 21 | % GUI_input=list of options in the GUI series.fig needed for the function |
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| 22 | % |
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| 23 | %INPUT: |
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| 24 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 25 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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| 26 | % In the absence of input (as activated when the current Action is selected |
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| 27 | % in series), the function ouput GUI_input set the activation of the needed GUI elements |
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| 28 | % |
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| 29 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
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| 30 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 31 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 32 | % .OutputSubDir: name of the subdirectory for data outputs |
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| 33 | % .OutputDir: directory for data outputs, including path |
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| 34 | % .Action: .ActionName: name of the current activated function |
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| 35 | % .ActionPath: path of the current activated function |
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| 36 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 37 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 38 | % .TransformPath: path of the selected transform function |
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| 39 | % .TransformHandle: corresponding function handle |
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| 40 | % .InputFields: sub structure describing the input fields withfields |
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| 41 | % .FieldName: name of the field |
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| 42 | % .VelType: velocity type |
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| 43 | % .FieldName_1: name of the second field in case of two input series |
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| 44 | % .VelType_1: velocity type of the second field in case of two input series |
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| 45 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 46 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 47 | |
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| 48 | |
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[374] | 49 | function GUI_input=sub_background (Param) |
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[24] | 50 | |
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[451] | 51 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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| 52 | if ~exist('Param','var') % case with no input parameter |
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| 53 | GUI_input={'NbViewMax';1;...% max nbre of input file series (default='' , no limitation) |
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| 54 | 'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default) |
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[24] | 55 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
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[451] | 56 | 'VelType';'off';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 57 | 'FieldName';'off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 58 | 'FieldTransform'; 'off';...%can use a transform function |
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| 59 | 'ProjObject';'off';...%can use projection object(option 'off'/'on', |
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| 60 | 'Mask';'off';...%can use mask option (option 'off'/'on', 'off' by default) |
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| 61 | 'OutputDirExt';'.sbk';...%set the output dir extension |
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[24] | 62 | ''}; |
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[451] | 63 | return |
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[24] | 64 | end |
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| 65 | |
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[451] | 66 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 67 | %% get input parameters, file names and indices |
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| 68 | % BATCH case: read the xml file for batch case |
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| 69 | if ischar(Param) && ~isempty(find(regexp(Param,'.xml$'))) |
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[374] | 70 | Param=xml2struct(Param); |
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[442] | 71 | checkrun=0; |
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[451] | 72 | % RUN case: parameters introduced as the input structure Param |
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| 73 | else |
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[374] | 74 | hseries=guidata(Param.hseries);%handles of the GUI series |
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[451] | 75 | WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series |
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| 76 | checkrun=1; % indicate the RUN option is used |
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[374] | 77 | end |
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[451] | 78 | % get the set of input file names (cell array filecell), and the lists of |
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| 79 | % input file or frame indices i1_series,i2_series,j1_series,j2_series |
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| 80 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 81 | % filecell{iview,fileindex}: cell array representing the list of file names |
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| 82 | % iview: line in the table corresponding to a given file series |
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| 83 | % fileindex: file index within the file series, |
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| 84 | % 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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| 85 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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| 86 | % set of frame indices used for movie or multimage input |
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| 87 | if ~isempty(j1_series) |
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| 88 | frame_index=j1_series; |
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| 89 | else |
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| 90 | frame_index=i1_series; |
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[24] | 91 | end |
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[394] | 92 | |
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[451] | 93 | %% root input file(s) and type |
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| 94 | RootPath=Param.InputTable(:,1); |
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| 95 | RootFile=Param.InputTable(:,3); |
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| 96 | SubDir=Param.InputTable(:,2); |
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| 97 | NomType=Param.InputTable(:,4); |
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| 98 | FileExt=Param.InputTable(:,5); |
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[89] | 99 | |
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[451] | 100 | % numbers of slices and file indices |
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| 101 | NbSlice=1;%default |
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| 102 | if isfield(Param.IndexRange,'NbSlice') |
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| 103 | NbSlice=Param.IndexRange.NbSlice; |
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[54] | 104 | end |
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[451] | 105 | nbview=size(i1_series,1);%number of input file series (lines in InputTable) |
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| 106 | nbfield_j=size(i1_series,2); %nb of consecutive fields at each level(burst |
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| 107 | nbfield=nbfield_j*size(i1_series,3); %total number of files or frames |
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| 108 | nbfield_i=floor(nbfield/NbSlice);%total number of i indexes (adjusted to an integer number of slices) |
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| 109 | nbfield=nbfield_i*nbfield_j; %total number of fields after adjustement |
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| 110 | |
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| 111 | %determine the file type on each line from the first input file |
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| 112 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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| 113 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 114 | |
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| 115 | % % for iview=1:nbview |
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| 116 | % if ~exist(filecell{iview,1}','file') |
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| 117 | % msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) |
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| 118 | % return |
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| 119 | % end |
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| 120 | % [FileType{iview},FileInfo{iview},Object{iview}]=get_file_type(filecell{iview,1}); |
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| 121 | % CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 122 | % CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 123 | % end |
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| 124 | |
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| 125 | [FileType,FileInfo,MovieObject]=get_file_type(filecell{1,1}); |
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| 126 | CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images |
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| 127 | |
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| 128 | %% calibration data and timing: read the ImaDoc files |
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| 129 | %not relevant here |
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| 130 | |
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| 131 | %% check coincidence in time for several input file series |
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| 132 | %not relevant here |
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| 133 | |
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| 134 | %% coordinate transform or other user defined transform |
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| 135 | %not relevant here |
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| 136 | |
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| 137 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 138 | % EDIT FROM HERE |
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| 139 | |
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| 140 | %% check the validity of input file types |
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| 141 | if CheckImage |
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| 142 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 143 | NomTypeOut='_1_1'; |
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| 144 | else |
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| 145 | msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image']) |
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[54] | 146 | return |
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| 147 | end |
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[451] | 148 | % |
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| 149 | % NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series |
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| 150 | % if NbSlice~=nbfield_j |
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| 151 | % answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]); |
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| 152 | % if ~strcmp(answer,'Yes') |
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| 153 | % return |
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| 154 | % end |
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| 155 | % end |
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[54] | 156 | |
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[451] | 157 | %% Set field names and velocity types |
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| 158 | %not relevant here |
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| 159 | |
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| 160 | |
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| 161 | %% Initiate output fields |
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| 162 | %not relevant here |
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| 163 | |
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| 164 | %%% SPECIFIC PART BEGINS HERE |
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| 165 | NbSlice=Param.IndexRange.NbSlice; %number of slices |
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| 166 | siz=size(i1_series); |
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[24] | 167 | 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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[394] | 168 | j1=[];%default |
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[24] | 169 | |
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[214] | 170 | %% apply the image rescaling function 'level' (avoid the blinking effects of bright particles) |
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| 171 | answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background'); |
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| 172 | test_level=isequal(answer,'Yes'); |
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| 173 | |
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| 174 | %% adjust the proposed number of images in the sliding average to include an integer number of bursts |
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[451] | 175 | if siz(3)~=1 |
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| 176 | nbaver=floor(nbaver_init/siz(2)); % number of bursts used for the sliding background, |
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[24] | 177 | if isequal(floor(nbaver/2),nbaver) |
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| 178 | nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined) |
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| 179 | end |
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[451] | 180 | nbaver_init=nbaver*siz(2);%propose by default an integer number of bursts |
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[24] | 181 | end |
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| 182 | |
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[214] | 183 | %% set processing parameters |
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[239] | 184 | prompt = {'Number of images for the sliding background (MUST FIT IN COMPUETER MEMORY)';'The number of positions (laser slices)';'volume scan mode (Yes/No)';... |
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[394] | 185 | 'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'}; |
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[451] | 186 | dlg_title = ['get (slice by slice) a sliding background and substract to each image, result in subdir ' Param.OutputDir]; |
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[24] | 187 | num_lines= 3; |
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[451] | 188 | def = { num2str(nbaver_init);num2str(NbSlice);'No';'0.1'}; |
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[24] | 189 | answer = inputdlg(prompt,dlg_title,num_lines,def); |
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| 190 | set(hseries.ParamVal,'String',answer([1 [3:4]])) |
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| 191 | set(hseries.ParamVal,'Visible','on') |
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| 192 | |
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| 193 | nbaver_ima=str2num(answer{1});%number of images for the sliding background |
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[451] | 194 | nbaver=ceil(nbaver_ima/siz(2));%number of bursts for the sliding background |
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[24] | 195 | if isequal(floor(nbaver/2),nbaver) |
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[394] | 196 | nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined) |
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[24] | 197 | end |
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[451] | 198 | step=siz(2);%case of bursts: the sliding background is shifted by one burst |
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[24] | 199 | vol_test=answer{3}; |
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| 200 | if isequal(vol_test,'Yes') |
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| 201 | nbfield2=1;%case of volume: no consecutive series at a given level |
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[451] | 202 | NbSlice=siz(2);%number of slices |
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[24] | 203 | else |
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[451] | 204 | nbfield2=siz(2); %nb of consecutive images at each level(burst) |
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| 205 | if siz(3)>1 |
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| 206 | % NbSlice=str2num(answer{2})/(num_i1(1,2)-num_i1(1,1));% number of slices |
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| 207 | NbSlice=str2num(answer{2})/(i1_series(1,1,2)-i1_series(1,1,1));% number of slices |
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[24] | 208 | else |
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[451] | 209 | NbSlice=1; |
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[24] | 210 | end |
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[451] | 211 | if ~isequal(floor(NbSlice),NbSlice) |
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[38] | 212 | msgbox_uvmat('ERROR','the number of slices must be a multiple of the i increment') |
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[24] | 213 | return |
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| 214 | end |
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| 215 | end |
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| 216 | rank=floor(str2num(answer{4})*nbaver_ima); |
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| 217 | if rank==0 |
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| 218 | rank=1;%rank selected in the sorted image series |
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| 219 | end |
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[451] | 220 | lengthtot=siz(2)*siz(3); |
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| 221 | nbfield=floor(lengthtot/(nbfield2*NbSlice));%total number of i indexes (adjusted to an integer number of slices) |
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[24] | 222 | nbfield_slice=nbfield*nbfield2;% number of fields per slice |
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| 223 | if nbaver_ima > nbfield*nbfield2 |
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[239] | 224 | msgbox_uvmat('ERROR','number of images in a slice smaller than the proposed number of images for the sliding average') |
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[24] | 225 | return |
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| 226 | end |
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| 227 | nbfirst=(ceil(nbaver/2))*step; |
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| 228 | if nbfirst>nbaver_ima |
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[214] | 229 | nbfirst=ceil(nbaver_ima/2); |
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[24] | 230 | step=1; |
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| 231 | nbaver=nbaver_ima; |
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| 232 | end |
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| 233 | |
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[239] | 234 | %% prealocate memory for the sliding background |
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[451] | 235 | Afirst=read_image(filecell{1,1},FileType{1},MovieObject,i1_series(1,1)); |
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[239] | 236 | [npy,npx]=size(Afirst); |
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[394] | 237 | try |
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| 238 | Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
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| 239 | Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
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[239] | 240 | catch ME |
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| 241 | msgbox_uvmat('ERROR',ME.message) |
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| 242 | return |
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| 243 | end |
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| 244 | |
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[442] | 245 | %% update the xml file |
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| 246 | SubDirBase=regexprep(Param.InputTable{1,2},'\..*','');%take the root part of SubDir, before the first dot '.' |
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[451] | 247 | filexml=fullfile(RootPath{1},[SubDirBase '.xml']); |
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[442] | 248 | if ~exist(filexml,'file') && exist([filebase '.xml'],'file')% xml inside the image directory |
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| 249 | copyfile([filebase '.xml'],filexml);% copy the .xml file |
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| 250 | end |
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| 251 | if exist(filexml,'file') |
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[447] | 252 | t=xmltree(filexml); |
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[24] | 253 | %update information on the first image name in the series |
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| 254 | uid_Heading=find(t,'ImaDoc/Heading'); |
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| 255 | if isempty(uid_Heading) |
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| 256 | [t,uid_Heading]=add(t,1,'element','Heading'); |
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[394] | 257 | end |
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[24] | 258 | uid_ImageName=find(t,'ImaDoc/Heading/ImageName'); |
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[394] | 259 | if ~isempty(j1_series{1}) |
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| 260 | j1=j1_series{1}(1); |
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| 261 | end |
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[451] | 262 | ImageName=fullfile_uvmat([dir_images term],'',RootFile{1},'.png',NomType,i1_series(1,1),[],j1); |
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[24] | 263 | [pth,ImageName]=fileparts(ImageName); |
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[239] | 264 | ImageName=[ImageName '.png']; |
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[24] | 265 | if isempty(uid_ImageName) |
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[394] | 266 | [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); |
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[24] | 267 | end |
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| 268 | uid_value=children(t,uid_ImageName); |
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| 269 | if isempty(uid_value) |
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[239] | 270 | t=add(t,uid_ImageName,'chardata',ImageName);%indicate name of the first image, with ;png extension |
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[24] | 271 | else |
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[239] | 272 | t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension |
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[394] | 273 | end |
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| 274 | |
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[24] | 275 | %add information about image transform |
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| 276 | [t,new_uid]=add(t,1,'element','ImageTransform'); |
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| 277 | [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction'); |
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[394] | 278 | [t]=add(t,NameFunction_uid,'chardata','sub_background'); |
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[217] | 279 | if test_level |
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[394] | 280 | [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction'); |
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| 281 | [t]=add(t,NameFunction_uid,'chardata','levels'); |
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[214] | 282 | end |
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[24] | 283 | [t,NbSlice_uid]=add(t,new_uid,'element','NbSlice'); |
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[451] | 284 | [t]=add(t,new_uid,'chardata',num2str(NbSlice)); |
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[24] | 285 | [t,NbSlidingImages_uid]=add(t,new_uid,'element','NbSlidingImages'); |
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| 286 | [t]=add(t,NbSlidingImages_uid,'chardata',num2str(nbaver)); |
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| 287 | [t,LuminosityRank_uid]=add(t,new_uid,'element','RankBackground'); |
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[394] | 288 | [t]=add(t,LuminosityRank_uid,'chardata',num2str(rank));% luminosity rank almong the nbaver sliding images |
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[442] | 289 | save(t,filexml) |
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[24] | 290 | end |
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| 291 | %copy the mask |
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[442] | 292 | % if exist([filebase '_1mask_1'],'file') |
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| 293 | % copyfile([filebase '_1mask_1'],[filebase_b '_1mask_1']);% copy the mask file |
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| 294 | % end |
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[24] | 295 | |
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| 296 | %MAIN LOOP ON SLICES |
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[451] | 297 | for islice=1:NbSlice |
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[214] | 298 | %% select the series of image indices at the level islice |
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[24] | 299 | for ifield=1:nbfield |
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| 300 | for iburst=1:nbfield2 |
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[451] | 301 | indselect(iburst,ifield)=((ifield-1)*NbSlice+(islice-1))*nbfield2+iburst; |
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[24] | 302 | end |
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[394] | 303 | end |
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[214] | 304 | |
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| 305 | %% read the first series of nbaver_ima images and sort by luminosity at each pixel |
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[24] | 306 | for ifield = 1:nbaver_ima |
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[54] | 307 | ifile=indselect(ifield); |
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[394] | 308 | filename=filecell{1,ifile}; |
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[451] | 309 | Aread=read_image(filename,FileType,MovieObject,i1_series{1}(ifile)); |
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[394] | 310 | Ak(:,:,ifield)=Aread; |
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[24] | 311 | end |
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| 312 | Asort=sort(Ak,3);%sort the luminosity of images at each point |
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| 313 | B=Asort(:,:,rank);%background image |
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[394] | 314 | display( 'first background image will be substracted') |
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[24] | 315 | for ifield=1:nbfirst |
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[394] | 316 | Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image |
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| 317 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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| 318 | C=uint16(Acor);% set to integer 16 bits |
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| 319 | ifile=indselect(ifield); |
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| 320 | % newname=name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',NomType)% makes the new file name |
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| 321 | if ~isempty(j1_series{1}) |
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| 322 | j1=j1_series{1}(ifile); |
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| 323 | end |
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[451] | 324 | newname=fullfile_uvmat(RootPath{1},Param.OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series(1,ifile),[],i_slice,[]); |
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| 325 | % newname=fullfile_uvmat(RootPath{1},SubdirResult,RootFile{1},'.png',NomType,i1_series{1}(ifile),[],j1); |
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[394] | 326 | %newname=name_generator(filebase_b,i1_series{1}(ifile),j1_series{1}(ifile),'.png',NomType);% makes the new file name |
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| 327 | if test_level |
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| 328 | C=levels(C); |
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| 329 | imwrite(C,newname,'BitDepth',8); % save the new image |
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| 330 | else |
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| 331 | imwrite(C,newname,'BitDepth',16); % save the new image |
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| 332 | end |
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[24] | 333 | end |
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[214] | 334 | |
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| 335 | %% repeat the operation on a sliding series of nbaver*nbfield2 images |
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| 336 | display('sliding background image will be substracted') |
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[24] | 337 | if nbfield_slice > nbaver_ima |
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| 338 | for ifield = step*ceil(nbaver/2)+1:step:nbfield_slice-step*floor(nbaver/2) |
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[442] | 339 | if checkrun |
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| 340 | stopstate=get(hseries.RUN,'BusyAction'); |
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[451] | 341 | update_waitbar(hseries.waitbar_frame,WaitbarPos,(ifield+(islice-1)*nbfield_slice)/(nbfield_slice*NbSlice)) |
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[442] | 342 | else |
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| 343 | stopstate='queue'; |
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| 344 | end |
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| 345 | if isequal(stopstate,'queue')% enable STOP command |
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[240] | 346 | Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step) |
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[24] | 347 | %incorporate next burst in the current image series |
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| 348 | for iburst=1:step |
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| 349 | ifile=indselect(ifield+step*floor(nbaver/2)+iburst-1); |
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[451] | 350 | filename=fullfile_uvmat(RootPath{1},SubDir,RootFile{1},FileExt,NomType,i1_series(1,ifile),[],j1_series(1,ifile)); |
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[442] | 351 | %filename=name_generator(filebase,num_i1(ifile),num_j1(ifile),FileExt,NomType); |
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[451] | 352 | Aread=read_image(filename,FileType,MovieObject,i1_series(1,ifile)); |
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[24] | 353 | Ak(:,:,nbaver_ima-step+iburst)=Aread; |
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| 354 | end |
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| 355 | Asort=sort(Ak,3);%sort the new current image series by luminosity |
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| 356 | B=Asort(:,:,rank);%current background image |
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| 357 | for iburst=1:step |
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| 358 | index=step*floor(nbaver/2)+iburst; |
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| 359 | Acor=double(Ak(:,:,index))-double(B); |
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| 360 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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| 361 | C=uint16(Acor); |
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| 362 | ifile=indselect(ifield+iburst-1); |
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[394] | 363 | if ~isempty(j1_series{1}) |
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| 364 | j1=j1_series{1}(ifile); |
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| 365 | end |
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[451] | 366 | newname=fullfile_uvmat(RootPath{1},Param.OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series(1,1),[],i_slice,[]); |
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| 367 | % newname=fullfile_uvmat(Param.InputTable{1,1},SubdirResult,Param.InputTable{1,3},'.png',NomType,i1_series{1}(ifile),[],j1); |
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[394] | 368 | %[newname]=name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',NomType) % makes the new file name |
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[214] | 369 | if test_level |
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| 370 | C=levels(C); |
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| 371 | imwrite(C,newname,'BitDepth',8); % save the new image |
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| 372 | else |
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| 373 | imwrite(C,newname,'BitDepth',16); % save the new image |
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| 374 | end |
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| 375 | end |
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[24] | 376 | else |
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| 377 | return |
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| 378 | end |
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| 379 | end |
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| 380 | end |
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[394] | 381 | |
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| 382 | %% substract the background from the last images |
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[214] | 383 | display('last background image will be substracted') |
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[394] | 384 | ifield=nbfield_slice-(step*ceil(nbaver/2))+1:nbfield_slice; |
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| 385 | for ifield=nbfield_slice-(step*floor(nbaver/2))+1:nbfield_slice |
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| 386 | index=ifield-nbfield_slice+step*(2*floor(nbaver/2)+1); |
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| 387 | Acor=double(Ak(:,:,index))-double(B); |
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| 388 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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| 389 | C=uint16(Acor); |
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| 390 | ifile=indselect(ifield); |
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| 391 | if ~isempty(j1_series{1}) |
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| 392 | j1=j1_series{1}(ifile); |
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| 393 | end |
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[451] | 394 | newname=fullfile_uvmat(RootPath{1},Param.OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series(1,ifile),[],j1); |
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| 395 | % newname=fullfile_uvmat(Param.InputTable{1,1},SubdirResult,Param.InputTable{1,3},'.png',NomType,i1_series{1}(ifile),[],j1); |
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[394] | 396 | if test_level |
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| 397 | C=levels(C); |
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| 398 | imwrite(C,newname,'BitDepth',8); % save the new image |
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| 399 | else |
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| 400 | imwrite(C,newname,'BitDepth',16); % save the new image |
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| 401 | end |
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| 402 | end |
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[24] | 403 | end |
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| 404 | |
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| 405 | %finish the waitbar |
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[442] | 406 | if checkrun |
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| 407 | update_waitbar(hseries.waitbar,WaitbarPos,1) |
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| 408 | end |
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[24] | 409 | |
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[54] | 410 | %------------------------------------------------------------------------ |
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| 411 | %--read images and convert them to the uint16 format used for PIV |
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[451] | 412 | function A=read_image(FileName,FileType,VideoObject,num) |
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[54] | 413 | %------------------------------------------------------------------------ |
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| 414 | %num is the view number needed for an avi movie |
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[451] | 415 | switch FileType |
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| 416 | case {'video','mmreader'} |
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| 417 | A=read(VideoObject,num); |
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[54] | 418 | case 'multimage' |
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[451] | 419 | A=imread(FileName,num); |
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[54] | 420 | case 'image' |
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[451] | 421 | A=imread(FileName); |
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[54] | 422 | end |
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| 423 | siz=size(A); |
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| 424 | if length(siz)==3;%color images |
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[451] | 425 | A=sum(double(A),3);% take the sum of color components |
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[54] | 426 | end |
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[24] | 427 | |
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[214] | 428 | |
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| 429 | function C=levels(A) |
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| 430 | %whos A; |
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| 431 | B=double(A(:,:,1)); |
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| 432 | windowsize=round(min(size(B,1),size(B,2))/20); |
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| 433 | windowsize=floor(windowsize/2)*2+1; |
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[239] | 434 | ix=1/2-windowsize/2:-1/2+windowsize/2;% |
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[214] | 435 | %del=np/3; |
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| 436 | %fct=exp(-(ix/del).^2); |
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| 437 | fct2=cos(ix/(windowsize-1)/2*pi/2); |
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| 438 | %Mfiltre=(ones(5,5)/5^2); |
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| 439 | %Mfiltre=fct2'; |
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| 440 | Mfiltre=fct2'*fct2; |
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| 441 | Mfiltre=Mfiltre/(sum(sum(Mfiltre))); |
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| 442 | |
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| 443 | C=filter2(Mfiltre,B); |
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| 444 | C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize); |
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| 445 | C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize); |
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| 446 | C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:); |
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| 447 | C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:); |
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| 448 | C=tanh(B./(2*C)); |
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| 449 | [n,c]=hist(reshape(C,1,[]),100); |
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| 450 | % figure;plot(c,n); |
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| 451 | |
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| 452 | [m,i]=max(n); |
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| 453 | c_max=c(i); |
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| 454 | [dummy,index]=sort(abs(c-c(i))); |
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| 455 | n=n(index); |
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| 456 | c=c(index); |
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| 457 | i_select = find(cumsum(n)<0.95*sum(n)); |
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| 458 | if isempty(i_select) |
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| 459 | i_select = 1:length(c); |
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| 460 | end |
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| 461 | c_select=c(i_select); |
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| 462 | n_select=n(i_select); |
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| 463 | cmin=min(c_select); |
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| 464 | cmax=max(c_select); |
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| 465 | C=(C-cmin)/(cmax-cmin)*256; |
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| 466 | C=uint8(C); |
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