1 | %'sub_background': substract a sliding background to an image series |
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2 | %------------------------------------------------------------------------ |
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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, |
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12 | % In the mode 'volume', nbfield2=1 (1 image at each level)and NbSlice (=nbfield_j) |
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13 | % Else nbfield2=nbfield_j =nbre of images in a burst (j index) |
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14 | |
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15 | % function GUI_config=sub_background(Param) |
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16 | % |
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17 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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18 | % |
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19 | %OUTPUT |
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20 | % ParamOut: sets options in the GUI series.fig needed for the function |
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21 | % |
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22 | %INPUT: |
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23 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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24 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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25 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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26 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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27 | % |
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28 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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29 | % 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 | % .OutputDirExt: directory extension for data outputs |
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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 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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37 | % .RUN =0 for GUI input, =1 for function activation |
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38 | % .RunMode='local','background', 'cluster': type of function use |
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39 | % |
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40 | % .IndexRange: set the file or frame indices on which the action must be performed |
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41 | % .FieldTransform: .TransformName: name of the selected transform function |
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42 | % .TransformPath: path of the selected transform function |
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43 | % .InputFields: sub structure describing the input fields withfields |
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44 | % .FieldName: name(s) of the field |
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45 | % .VelType: velocity type |
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46 | % .FieldName_1: name of the second field in case of two input series |
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47 | % .VelType_1: velocity type of the second field in case of two input series |
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48 | % .Coord_y: name of y coordinate variable |
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49 | % .Coord_x: name of x coordinate variable |
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50 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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51 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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52 | |
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53 | %======================================================================= |
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54 | % Copyright 2008-2020, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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55 | % http://www.legi.grenoble-inp.fr |
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56 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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57 | % |
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58 | % This file is part of the toolbox UVMAT. |
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59 | % |
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60 | % UVMAT is free software; you can redistribute it and/or modify |
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61 | % it under the terms of the GNU General Public License as published |
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62 | % by the Free Software Foundation; either version 2 of the license, |
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63 | % or (at your option) any later version. |
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64 | % |
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65 | % UVMAT is distributed in the hope that it will be useful, |
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66 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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67 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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68 | % GNU General Public License (see LICENSE.txt) for more details. |
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69 | %======================================================================= |
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70 | |
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71 | function ParamOut=sub_background (Param) |
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72 | |
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73 | %%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% |
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74 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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75 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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76 | ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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77 | ParamOut.NbSlice='on'; % edit box nbre of slices made active |
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78 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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79 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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80 | ParamOut.FieldTransform = 'off';%can use a transform function |
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81 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', |
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82 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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83 | ParamOut.OutputDirExt='.sback';%set the output dir extension |
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84 | ParamOut.OutputFileMode='NbInput';% '=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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85 | |
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86 | %% root input file(s) and type |
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87 | % check the existence of the first file in the series |
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88 | first_j=[];% note that the function will propose to cover the whole range of indices |
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89 | if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end |
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90 | last_j=[]; |
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91 | if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end |
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92 | PairString=''; |
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93 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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94 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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95 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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96 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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97 | if ~exist(FirstFileName,'file') |
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98 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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99 | else |
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100 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); |
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101 | LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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102 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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103 | if ~exist(FirstFileName,'file') |
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104 | msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) |
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105 | end |
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106 | end |
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107 | |
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108 | %% check the validity of input file types |
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109 | FileInfo=get_file_info(FirstFileName); |
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110 | FileType=FileInfo.FileType; |
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111 | CheckImage=strcmp(FileInfo.FieldType,'image');% =1 for images |
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112 | if ~CheckImage |
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113 | msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not an image']) |
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114 | return |
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115 | end |
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116 | |
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117 | %% numbers of fields |
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118 | NbSlice_i=1;%default |
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119 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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120 | NbSlice_i=Param.IndexRange.NbSlice; |
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121 | end |
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122 | incr_j=1;%default |
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123 | if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j) |
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124 | incr_j=Param.IndexRange.incr_j; |
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125 | end |
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126 | if isempty(first_j)||isempty(last_j) |
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127 | nbfield_j=1; |
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128 | else |
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129 | nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices) |
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130 | end |
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131 | first_i=1;last_i=1;incr_i=1;%default |
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132 | if isfield(Param.IndexRange,'MinIndex_i'); first_i=Param.IndexRange.MinIndex_i; end |
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133 | if isfield(Param.IndexRange,'MaxIndex_i'); last_i=Param.IndexRange.MaxIndex_i; end |
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134 | if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i) |
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135 | incr_i=Param.IndexRange.incr_i; |
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136 | end |
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137 | nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices) |
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138 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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139 | nbfield_i=floor(nbfield/NbSlice_i);%total number of indexes in a slice (adjusted to an integer number of slices) |
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140 | |
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141 | %% setting of parameters specific to sub_background |
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142 | CheckVolume='No'; |
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143 | nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts |
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144 | if nbfield_i~=1 |
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145 | nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background, |
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146 | if isequal(mod(nbaver,2),0)% if nbaver is even |
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147 | nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined) |
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148 | end |
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149 | nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts |
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150 | end |
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151 | BrightnessRankThreshold=0.1; |
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152 | CheckSubmedian='No'; |
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153 | SaturationCoeff=0; |
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154 | if isfield(Param,'ActionInput') |
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155 | if isfield(Param.ActionInput,'CheckVolume') && Param.ActionInput.CheckVolume |
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156 | CheckVolume='Yes'; |
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157 | end |
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158 | if isfield(Param.ActionInput,'SlidingSequenceLength') |
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159 | nbaver_init=Param.ActionInput.SlidingSequenceLength; |
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160 | end |
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161 | if isfield(Param.ActionInput,'BrightnessRankThreshold') |
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162 | BrightnessRankThreshold=Param.ActionInput.BrightnessRankThreshold; |
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163 | end |
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164 | if isfield(Param.ActionInput,'CheckSubmedian') && Param.ActionInput.CheckSubmedian |
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165 | CheckSubmedian='Yes'; |
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166 | end |
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167 | if isfield(Param.ActionInput,'SaturationCoeff') |
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168 | SaturationCoeff=Param.ActionInput.SaturationCoeff; |
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169 | end |
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170 | end |
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171 | prompt = {'volume scan mode (Yes/No)';... |
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172 | 'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';... |
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173 | 'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles';... |
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174 | 'set to 0 image levels below median(Yes/No)';... |
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175 | 'image rescaling coefficient(=2 to reduce the influence of bright particles), =0 for no rescaling' }; |
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176 | dlg_title = 'get (slice by slice) a sliding background and substract to each image'; |
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177 | num_lines= 5; |
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178 | def = { CheckVolume;num2str(nbaver_init);num2str(BrightnessRankThreshold);CheckSubmedian;num2str(SaturationCoeff)}; |
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179 | answer = inputdlg(prompt,dlg_title,num_lines,def); |
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180 | if isempty(answer) |
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181 | return |
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182 | end |
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183 | %check input consistency |
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184 | if strcmp(answer{1},'No') && ~isequal(NbSlice_i,1) |
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185 | check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice_i) ' slices']); |
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186 | if ~strcmp(check,'Yes') |
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187 | return |
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188 | end |
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189 | end |
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190 | if strcmp(answer{1},'Yes') |
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191 | step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume ;ode |
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192 | ParamOut.NbSlice=1; %nbre of slices displayed |
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193 | else |
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194 | step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst |
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195 | end |
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196 | nbaver_ima=str2double(answer{2});%number of images for the sliding background |
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197 | nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background |
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198 | if isequal(mod(nbaver,2),0)% if nbaver is even |
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199 | nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) |
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200 | end |
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201 | nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver |
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202 | ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes'); |
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203 | ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima; |
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204 | ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3}); |
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205 | ParamOut.ActionInput.CheckSubmedian=strcmp(answer{4},'Yes'); |
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206 | ParamOut.ActionInput.SaturationCoeff=str2double(answer{5}); |
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207 | % apply the image rescaling function 'level' (avoid the blinking effects of bright particles) |
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208 | % answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background'); |
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209 | % ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes'); |
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210 | return |
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211 | end |
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212 | %%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% |
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213 | |
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214 | %% read input parameters from an xml file if input is a file name (batch mode) |
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215 | checkrun=1; |
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216 | RUNHandle=[]; |
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217 | WaitbarHandle=[]; |
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218 | if ischar(Param) |
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219 | Param=xml2struct(Param);% read Param as input file (batch case) |
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220 | checkrun=0; |
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221 | else |
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222 | hseries=findobj(allchild(0),'Tag','series'); |
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223 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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224 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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225 | end |
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226 | |
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227 | %% input preparation |
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228 | NbSlice_i=Param.IndexRange.NbSlice; |
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229 | if ~isequal(NbSlice_i,1) |
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230 | display(['multi-level splitting into ' num2str(NbSlice_i) ' slices']); |
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231 | end |
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232 | RootPath=Param.InputTable(:,1); |
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233 | RootFile=Param.InputTable(:,3); |
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234 | SubDir=Param.InputTable(:,2); |
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235 | NomType=Param.InputTable(:,4); |
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236 | FileExt=Param.InputTable(:,5); |
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237 | %hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); |
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238 | [filecell,i1_series,i2_series,j1_series]=get_file_series(Param); |
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239 | % if ~isempty(hdisp),delete(hdisp),end; |
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240 | %%%%%%%%%%%% |
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241 | % The cell array filecell is the list of input file names, while |
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242 | % filecell{iview,fileindex}: |
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243 | % iview: line in the table corresponding to a given file series |
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244 | % fileindex: file index within the file series, |
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245 | % 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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246 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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247 | %%%%%%%%%%%% |
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248 | [FileInfo{1},MovieObject{1}]=get_file_info(filecell{1,1}); |
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249 | FileType{1}=FileInfo{1}.FileType; |
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250 | if ~isempty(j1_series{1}) |
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251 | frame_index{1}=j1_series{1}; |
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252 | else |
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253 | frame_index{1}=i1_series{1}; |
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254 | end |
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255 | |
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256 | |
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257 | %% output file naming |
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258 | FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image' |
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259 | if strcmp(FileInfo{1}.FileType,'image') |
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260 | NomTypeOut=NomType{1}; |
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261 | % if strcmp(lower(NomType{1}(end)),'a') |
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262 | % NomTypeOut=NomType{1};%case of letter appendix |
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263 | elseif isempty(j1_series{1}) |
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264 | NomTypeOut='_1'; |
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265 | else |
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266 | NomTypeOut='_1_1';% caseof purely numerical indexing |
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267 | end |
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268 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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269 | |
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270 | %% file index parameters |
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271 | % NbSlice_i: nbre of slices for i index: different of of 1 for multi-level, |
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272 | % the function sub_background is then relaunched by the GUI series for each |
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273 | % slice, incrementing the first index i by 1 |
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274 | % NbSlice_j: nbre of slices in volume mode |
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275 | % nbfield : total number of images treated per slice |
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276 | % step: shift of image index at each step of the sliding background (corresponding to the nbre of images in a burst) |
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277 | % nbaver_ima: nbre of the images in the sliding sequence used for the background |
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278 | % nbaver=nbaver_ima/step: nbre of bursts corresponding to nbaver_ima images. It has been adjusted so that nbaver is an odd integer |
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279 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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280 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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281 | |
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282 | if Param.ActionInput.CheckVolume |
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283 | step=2;% we assume the burst contains only one image pair |
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284 | NbSlice_j=nbfield_j; |
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285 | NbSlice=nbfield_j; |
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286 | nbfield_series=nbfield_i; |
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287 | else |
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288 | step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst |
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289 | NbSlice_j=1; |
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290 | NbSlice=NbSlice_i; |
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291 | %nbfield_i=floor(nbfield_i/NbSlice_i);%total number of indexes in a slice (adjusted to an integer number of slices) |
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292 | %nbfield=nbfield_i*NbSlice_i; %total number of fields after adjustement |
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293 | nbfield_series=nbfield_i*nbfield_j; |
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294 | end |
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295 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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296 | nbaver_ima=Param.ActionInput.SlidingSequenceLength;%number of images for the sliding background |
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297 | nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background |
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298 | if isequal(mod(nbaver,2),0) |
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299 | nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) |
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300 | end |
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301 | nbaver_ima=nbaver*step; |
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302 | if nbaver_ima > nbfield |
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303 | display('number of images in a slice smaller than the proposed number of images for the sliding average') |
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304 | return |
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305 | end |
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306 | halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background |
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307 | |
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308 | %% calculate absolute brightness rank |
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309 | rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima); |
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310 | if rank==0 |
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311 | rank=1;%rank selected in the sorted image series |
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312 | end |
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313 | |
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314 | %% prealocate memory for the sliding background |
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315 | try |
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316 | Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1)); |
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317 | [npy,npx,nbcolor]=size(Afirst);% the argument nbcolor is important to get npx right for color images |
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318 | if strcmp(class(Afirst),'uint8') % case of 8bit images |
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319 | Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory |
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320 | Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory |
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321 | else |
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322 | Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
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323 | Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
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324 | end |
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325 | catch ME |
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326 | msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message]) |
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327 | return |
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328 | end |
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329 | |
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330 | |
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331 | %%%%%%% LOOP ON SLICES FOR VOLUME SCAN %%%%%%% |
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332 | for j_slice=1:NbSlice_j |
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333 | %% select the series of i indices to process |
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334 | indselect=j_slice:step*NbSlice_j:nbfield;% select file indices of the slice |
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335 | for ifield=1:step-1 |
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336 | indselect=[indselect;indselect(end,:)+NbSlice_j]; |
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337 | end |
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338 | |
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339 | %% read the first series of nbaver_ima images and sort by luminosity at each pixel |
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340 | for ifield = 1:nbaver_ima |
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341 | ifile=indselect(ifield); |
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342 | filename=filecell{1,ifile}; |
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343 | Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); |
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344 | if ndims(Aread)==3;%color images |
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345 | Aread=sum(double(Aread),3);% take the sum of color components |
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346 | end |
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347 | Ak(:,:,ifield)=Aread; |
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348 | end |
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349 | Asort=sort(Ak,3);%sort the luminosity of images at each point |
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350 | B=Asort(:,:,rank);%background image |
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351 | |
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352 | %% substract the first background image to the first images |
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353 | display( 'first background image will be substracted') |
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354 | for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image |
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355 | Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image |
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356 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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357 | ifile=indselect(ifield); |
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358 | j1=1; |
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359 | if ~isempty(j1_series{1}) |
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360 | j1=j1_series{1}(ifile); |
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361 | end |
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362 | newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
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363 | |
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364 | %write result file |
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365 | if ~isequal(Param.ActionInput.SaturationCoeff,0) |
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366 | C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff); |
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367 | imwrite(C,newname,'BitDepth',16); % save the new image |
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368 | else |
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369 | if ~isfield(FileInfo{1},'BitDepth') |
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370 | FileInfo{1}.BitDepth=16; |
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371 | end |
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372 | if isequal(FileInfo{1}.BitDepth,16) |
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373 | C=uint16(Acor); |
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374 | imwrite(C,newname,'BitDepth',16); % save the new image |
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375 | else |
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376 | C=uint8(Acor); |
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377 | imwrite(C,newname,'BitDepth',8); % save the new image |
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378 | end |
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379 | end |
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380 | display([newname ' written']) |
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381 | end |
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382 | |
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383 | %% repeat the operation on a sliding series of images |
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384 | display('sliding background image will be substracted') |
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385 | if nbfield_series > nbaver_ima |
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386 | for ifield = step*(halfnbaver+1):step:nbfield_series-step*(halfnbaver+1)% ifield +iburst=index of the current processed image |
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387 | update_waitbar(WaitbarHandle,ifield/nbfield_series) |
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388 | if ~isempty(RUNHandle)&&~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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389 | disp('program stopped by user') |
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390 | return |
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391 | end |
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392 | if nbaver_ima>step |
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393 | Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step) |
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394 | end |
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395 | %incorporate next burst in the current image series |
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396 | for iburst=1:step |
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397 | ifile=indselect(ifield+iburst+step*halfnbaver); |
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398 | j1=1; |
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399 | if ~isempty(j1_series{1}) |
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400 | j1=j1_series{1}(ifile); |
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401 | end |
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402 | filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1); |
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403 | Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); |
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404 | if ndims(Aread)==3;%color images |
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405 | Aread=sum(double(Aread),3);% take the sum of color components |
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406 | end |
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407 | Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image |
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408 | end |
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409 | Asort=sort(Ak,3);%sort the new current image series by luminosity |
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410 | B=Asort(:,:,rank);%current background image |
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411 | %substract the background for the current burst |
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412 | for iburst=1:step |
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413 | Acor=double(Ak(:,:,step*halfnbaver+iburst))-double(B); %the current image has been already read ans stored as index step*halfnbaver+iburst in the current series |
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414 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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415 | ifile=indselect(ifield+iburst); |
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416 | if ~isempty(j1_series{1}) |
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417 | j1=j1_series{1}(ifile); |
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418 | end |
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419 | newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
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420 | %write result file |
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421 | if ~isequal(Param.ActionInput.SaturationCoeff,0) |
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422 | C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff); |
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423 | imwrite(C,newname,'BitDepth',16); % save the new image |
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424 | else |
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425 | if isequal(FileInfo{1}.BitDepth,16) |
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426 | C=uint16(Acor); |
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427 | imwrite(C,newname,'BitDepth',16); % save the new image |
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428 | else |
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429 | C=uint8(Acor); |
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430 | imwrite(C,newname,'BitDepth',8); % save the new image |
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431 | end |
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432 | end |
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433 | display([newname ' written']) |
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434 | end |
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435 | end |
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436 | end |
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437 | |
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438 | %% substract the background from the last images |
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439 | display('last background image will be substracted') |
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440 | for ifield=nbfield_series-step*halfnbaver+1:nbfield_series |
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441 | Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B); |
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442 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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443 | ifile=indselect(ifield); |
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444 | if ~isempty(j1_series{1}) |
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445 | j1=j1_series{1}(ifile); |
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446 | end |
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447 | newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
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448 | %write result file |
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449 | if ~isequal(Param.ActionInput.SaturationCoeff,0) |
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450 | C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff); |
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451 | imwrite(C,newname,'BitDepth',16); % save the new image |
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452 | else |
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453 | if isequal(FileInfo{1}.BitDepth,16) |
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454 | C=uint16(Acor); |
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455 | imwrite(C,newname,'BitDepth',16); % save the new image |
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456 | else |
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457 | C=uint8(Acor); |
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458 | imwrite(C,newname,'BitDepth',8); % save the new image |
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459 | end |
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460 | end |
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461 | display([newname ' written']) |
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462 | end |
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463 | end |
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464 | |
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465 | function C=levels(A,CheckSubmedian,Coeff) |
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466 | |
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467 | nblock_y=100;%2*Param.TransformInput.BlockSize; |
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468 | nblock_x=100;%2*Param.TransformInput.BlockSize; |
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469 | [npy,npx]=size(A); |
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470 | [X,Y]=meshgrid(1:npx,1:npy); |
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471 | |
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472 | %Backg=zeros(size(A)); |
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473 | %Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima |
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474 | %Amin=A.*Aflagmin;%values of A at local minima |
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475 | % local background: find all the local minima in image subblocks |
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476 | if CheckSubmedian |
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477 | fctblock= inline('median(x(:))'); |
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478 | Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in blocks |
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479 | %B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image |
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480 | A=A-imresize(Backg,size(A),'bilinear');% substract background interpolated to the initial size image |
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481 | end |
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482 | fctblock= inline('mean(x(:))'); |
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483 | AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in blocks |
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484 | fctblock= inline('var(x(:))'); |
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485 | AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in blocks |
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486 | Avalue=AVar./AMean;% typical value of particle luminosity |
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487 | Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image |
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488 | C=uint16(1000*tanh(A./(Coeff*Avalue))); |
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