1 | % function ParamOut=particle_tracking(Param) |
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2 | % |
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3 | % Method: |
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4 | |
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5 | % Organization of image indices: |
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6 | |
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7 | %INPUT: |
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8 | % num_i1: matrix of image indices i |
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9 | % num_j1: matrix of image indices j, must be the same size as num_i1 |
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10 | % num_i2 and num_j2: not used for a function acting on images |
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11 | % Series: matlab structure containing parameters, as defined by the interface UVMAT/series |
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12 | % Series.RootPath{1}: path to the image series |
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13 | % Series.RootFile{1}: root file name |
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14 | % Series.FileExt{1}: image file extension |
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15 | % Series.NomType{1}: nomenclature type for file in |
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16 | % |
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17 | % Method: |
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18 | % Series.NbSlice: %number of slices defined on the interface |
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19 | % global A rangx0 rangy0 minA maxA; % make current image A accessible in workspace |
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20 | % global hfig1 hfig2 scalar |
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21 | % global Abackg nbpart lum diam |
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22 | %%%%%%%%%%%%%%ï¿œ |
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23 | % |
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24 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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25 | % |
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26 | %OUTPUT |
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27 | % ParamOut: sets options in the GUI series.fig needed for the function |
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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 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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33 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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34 | % |
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35 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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36 | % see the current structure Param) |
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37 | % .InputTable: cell of input file names, (several lines for multiple input) |
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38 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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39 | % .OutputSubDir: name of the subdirectory for data outputs |
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40 | % .OutputDirExt: directory extension for data outputs |
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41 | % .Action: .ActionName: name of the current activated function |
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42 | % .ActionPath: path of the current activated function |
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43 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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44 | % .RUN =0 for GUI input, =1 for function activation |
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45 | % .RunMode='local','background', 'cluster': type of function use |
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46 | % |
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47 | % .IndexRange: set the file or frame indices on which the action must be performed |
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48 | % .FieldTransform: .TransformName: name of the selected transform function |
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49 | % .TransformPath: path of the selected transform function |
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50 | % .InputFields: sub structure describing the input fields withfields |
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51 | % .FieldName: name(s) of the field |
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52 | % .VelType: velocity type |
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53 | % .FieldName_1: name of the second field in case of two input series |
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54 | % .VelType_1: velocity type of the second field in case of two input series |
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55 | % .Coord_y: name of y coordinate variable |
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56 | % .Coord_x: name of x coordinate variable |
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57 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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58 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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59 | |
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60 | %======================================================================= |
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61 | % Copyright 2008-2021, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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62 | % http://www.legi.grenoble-inp.fr |
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63 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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64 | % |
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65 | % This file is part of the toolbox UVMAT. |
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66 | % |
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67 | % UVMAT is free software; you can redistribute it and/or modify |
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68 | % it under the terms of the GNU General Public License as published |
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69 | % by the Free Software Foundation; either version 2 of the license, |
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70 | % or (at your option) any later version. |
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71 | % |
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72 | % UVMAT is distributed in the hope that it will be useful, |
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73 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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74 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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75 | % GNU General Public License (see LICENSE.txt) for more details. |
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76 | %======================================================================= |
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77 | |
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78 | function ParamOut=particle_tracking(Param) |
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79 | |
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80 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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81 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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82 | % general settings of the GUI: |
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83 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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84 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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85 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default) |
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86 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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87 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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88 | ParamOut.FieldTransform = 'off';%can use a transform function |
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89 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', |
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90 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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91 | ParamOut.OutputDirExt='.track';%set the output dir extension |
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92 | ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice |
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93 | filecell=get_file_series(Param);%check existence of the first input file |
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94 | if ~exist(filecell{1,1},'file') |
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95 | msgbox_uvmat('WARNING','the first input file does not exist') |
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96 | end |
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97 | % parameters specific to the function 'particle_tracking' |
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98 | Par.Nblock=10;%size of image subblocks for background determination, =[]: no sublock |
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99 | Par.ThreshLum=210;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles |
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100 | ParamOut.ActionInput=Par; |
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101 | return |
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102 | end |
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103 | |
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104 | %%%%%%%%%%%% STANDARD RUN PART %%%%%%%%%%%% |
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105 | ParamOut=[]; |
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106 | %% read input parameters from an xml file if input is a file name (batch mode) |
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107 | checkrun=1; |
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108 | if ischar(Param) |
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109 | Param=xml2struct(Param);% read Param as input file (batch case) |
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110 | checkrun=0; |
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111 | end |
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112 | hseries=findobj(allchild(0),'Tag','series'); |
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113 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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114 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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115 | |
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116 | %% define the directory for result file |
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117 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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118 | |
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119 | %% root input file(s) name, type and index series |
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120 | RootPath=Param.InputTable{1,1}; |
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121 | RootFile=Param.InputTable{1,3}; |
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122 | SubDir=Param.InputTable{1,2}; |
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123 | NomType=Param.InputTable{1,4}; |
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124 | FileExt=Param.InputTable{1,5}; |
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125 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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126 | %%%%%%%%%%%% |
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127 | % The cell array filecell is the list of input file names, while |
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128 | % filecell{iview,fileindex}: |
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129 | % iview: line in the table corresponding to a given file series |
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130 | % fileindex: file index within the file series, |
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131 | % 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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132 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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133 | %%%%%%%%%%%% |
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134 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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135 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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136 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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137 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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138 | |
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139 | %% frame index for movie or multimage file input |
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140 | if ~isempty(j1_series{1}) |
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141 | frame_index=j1_series{1}; |
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142 | else |
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143 | frame_index=i1_series{1}; |
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144 | end |
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145 | |
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146 | %% check the input file type |
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147 | [FileInfo,VideoObject]=get_file_info(filecell{1,1}); |
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148 | FileType=FileInfo.FileType; |
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149 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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150 | if isempty(find(strcmp(FileType,ImageTypeOptions))) |
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151 | disp('input file not images') |
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152 | return |
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153 | end |
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154 | |
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155 | %% calibration data and timing: read the ImaDoc files |
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156 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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157 | |
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158 | %%%%%%%%%%%% SPECIFIC PART (to edit) %%%%%%%%%%%% |
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159 | %filter for particle center of mass(luminosity) |
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160 | %Nblock=Param.ActionInput.Nblock; |
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161 | ThreshLum=Param.ActionInput.ThreshLum;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles |
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162 | %AbsThreshold=30; %threshold below which a pixel is considered belonging to a float |
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163 | SizePart=4; |
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164 | % |
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165 | hh=ones(5,5); |
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166 | hh(1,1)=0; |
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167 | hh(1,5)=0;% sum luminosity on the 5x5 domain without corners |
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168 | hh(5,1)=0; |
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169 | hh(5,5)=0; |
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170 | hdx=[-2:1:2]; |
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171 | hdy=[-2:1:2]; |
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172 | [hdX,hdY]=meshgrid(hdx,hdy); |
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173 | hdX(1,1)=0; |
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174 | hdX(1,5)=0;% sum luminosity on the 5x5 domain -corners |
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175 | hdX(5,1)=0; |
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176 | hdX(5,5)=0; |
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177 | hdY(1,1)=0; |
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178 | hdY(1,5)=0;% sum luminosity on the 5x5 domain -corners |
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179 | hdY(5,1)=0; |
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180 | hdY(5,5)=0; |
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181 | |
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182 | %% detection of particles on the first image |
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183 | |
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184 | %%%%%% MAIN LOOP ON FRAMES %%%%%% |
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185 | for ifile=1:nbfield |
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186 | if checkrun |
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187 | update_waitbar(WaitbarHandle,ifile/nbfield) |
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188 | if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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189 | disp('program stopped by user') |
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190 | return |
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191 | end |
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192 | end |
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193 | j1=[]; |
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194 | if ~isempty(j1_series)&&~isequal(j1_series,{[]}) |
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195 | j1=j1_series{1}(ifile); |
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196 | end |
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197 | filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series{1}(ifile),[],j1); |
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198 | A=read_image(filename,FileType,VideoObject,frame_index(ifile));% read the current frame |
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199 | if ndims(A)==3;%color images |
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200 | A=sum(double(A),3);% take the sum of color components |
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201 | end |
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202 | %% mask to reduce the working area (optional) |
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203 | Mask=ones(size(A)); |
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204 | Mask(1:SizePart,:)=0; |
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205 | Mask(end-SizePart:end,:)=0; |
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206 | Mask(:,1:SizePart)=0; |
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207 | Mask(:,end-SizePart:end)=0; |
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208 | if ifile ==1 |
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209 | if ThreshLum>0 %brigth particles |
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210 | [Js,Is]=find(A>ThreshLum & Mask==1);%indices (I,J) of dark pixels |
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211 | else %black particle |
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212 | [Js,Is]=find(A<ThreshLum & Mask==1);%indices (I,J) of dark pixels |
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213 | end |
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214 | else |
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215 | Is=round(Xtime(ifile-1,:)); |
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216 | Js=round(Ytime(ifile-1,:)); |
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217 | end |
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218 | X=zeros(size(Is)); |
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219 | Y=zeros(size(Js)); |
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220 | F=zeros(size(Js)); |
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221 | for ipart=1:numel(Is) |
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222 | if Mask(Js(ipart),Is(ipart))==1 |
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223 | subimage=A(Js(ipart)-SizePart:Js(ipart)+SizePart,Is(ipart)-SizePart:Is(ipart)+SizePart); |
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224 | subimage=max(max(subimage))-subimage;%take negative of the image |
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225 | [vector,F(ipart)] = SUBPIX2DGAUSS (subimage,SizePart+1,SizePart+1); |
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226 | % X0(ipart)=Is(ipart);%TEST |
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227 | % Y0(ipart)=Js(ipart);%TEST |
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228 | X(ipart)=Is(ipart)+vector(1);%corrected position |
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229 | Y(ipart)=Js(ipart)+vector(2); |
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230 | Xround=round(X(ipart)); |
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231 | Yround=round(Y(ipart)); |
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232 | if ifile==1 |
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233 | Mask(Yround-SizePart:Yround+SizePart,Xround-SizePart:Xround+SizePart)=0;% mask the subregion already treated to |
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234 | % avoid double counting |
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235 | end |
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236 | end |
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237 | end |
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238 | % X0=X0(X>0); |
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239 | % Y0=Y0(Y>0); |
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240 | if ifile ==1 |
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241 | Ftime(1,:)=F(X>0); |
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242 | Xtime(1,:)=X(X>0); |
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243 | Ytime(1,:)=Y(Y>0); |
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244 | else |
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245 | Ftime(ifile,:)=F; |
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246 | Xtime(ifile,:)=X; |
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247 | Ytime(ifile,:)=Y; |
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248 | end |
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249 | end |
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250 | figure(1) |
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251 | plot(Xtime) |
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252 | figure(2) |
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253 | plot(Ytime) |
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254 | |
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255 | %------------------------------------------------------------------------ |
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256 | % --- Find the maximum of the correlation function after interpolation |
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257 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
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258 | %------------------------------------------------------------------------ |
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259 | vector=[0 0]; %default |
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260 | F=-2; |
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261 | peaky=y; |
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262 | peakx=x; |
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263 | [npy,npx]=size(result_conv); |
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264 | if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) |
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265 | F=0; |
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266 | for i=-1:1 |
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267 | for j=-1:1 |
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268 | %following 15 lines based on |
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269 | %H. Nobach ï¿œ M. Honkanen (2005) |
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270 | %Two-dimensional Gaussian regression for sub-pixel displacement |
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271 | %estimation in particle image velocimetry or particle position |
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272 | %estimation in particle tracking velocimetry |
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273 | %Experiments in Fluids (2005) 38: 511ï¿œ515 |
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274 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
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275 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
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276 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
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277 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
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278 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
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279 | end |
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280 | end |
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281 | c10=(1/6)*sum(sum(c10)); |
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282 | c01=(1/6)*sum(sum(c01)); |
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283 | c11=(1/4)*sum(sum(c11)); |
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284 | c20=(1/6)*sum(sum(c20)); |
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285 | c02=(1/6)*sum(sum(c02)); |
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286 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
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287 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
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288 | if abs(deltax)<1 |
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289 | peakx=x+deltax; |
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290 | end |
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291 | if abs(deltay)<1 |
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292 | peaky=y+deltay; |
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293 | end |
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294 | end |
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295 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
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296 | |
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