1 | %'sub_background': substract background to an image series, used with series.fig |
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2 | %------------------------------------------------------------------------ |
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3 | % function GUI_input=aver_stat(num_i1,num_i2,num_j1,num_j2,Series) |
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4 | % |
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5 | %OUTPUT |
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6 | % GUI_input=list of options in the GUI series.fig needed for the function |
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7 | % |
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8 | %INPUT: |
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9 | %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
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10 | %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
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11 | %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) |
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12 | %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) |
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13 | %Series: Matlab structure containing information set by the series interface |
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14 | % .RootPath: path to the image series |
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15 | % .RootFile: root file name |
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16 | % .FileExt: image file extension |
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17 | % .NomType: nomenclature type for file indexing |
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18 | % .NbSlice: %number of slices defined on the interface |
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19 | %---------------------------------------------------------------------- |
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20 | % Method: |
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21 | % calculate the background image by sorting the luminosity of each point |
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22 | % over a sliding sub-sequence of 'nbaver_ima' images. |
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23 | % The luminosity value of rank 'rank' is selected as the |
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24 | % 'background'. rank=nbimages/2 gives the median value. Smaller values are appropriate |
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25 | % for a dense set of particles. The extrem value rank=1 gives the true minimum |
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26 | % luminosity, but it can be polluted by noise. |
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27 | % Organization of image indices: |
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28 | % The program is working on a series of images, labelled by two indices i and j, given |
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29 | % by the input matlab vectors num_i1 and num_j1 respectively. In the list, j is the fastest increasing index. |
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30 | % The processing can be done in slices (number nbslice), with bursts of |
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31 | % nbfield2 successive images for a given slice (mode 'multilevel') |
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32 | % In the mode 'volume', nbfield2=1 (1 image at each level) |
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33 | |
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34 | %======================================================================= |
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35 | % Copyright 2008-2018, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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36 | % http://www.legi.grenoble-inp.fr |
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37 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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38 | % |
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39 | % This file is part of the toolbox UVMAT. |
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40 | % |
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41 | % UVMAT is free software; you can redistribute it and/or modify |
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42 | % it under the terms of the GNU General Public License as published |
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43 | % by the Free Software Foundation; either version 2 of the license, |
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44 | % or (at your option) any later version. |
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45 | % |
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46 | % UVMAT is distributed in the hope that it will be useful, |
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47 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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48 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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49 | % GNU General Public License (see LICENSE.txt) for more details. |
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50 | %======================================================================= |
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51 | |
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52 | function GUI_input=calc_background (num_i1,num_i2,num_j1,num_j2,Series) |
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53 | |
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54 | %------------------------------------------------------------------------ |
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55 | %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) |
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56 | if ~exist('num_i1','var') |
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57 | GUI_input={'RootPath';'on';... |
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58 | 'SubDir';'off';... % subdirectory of derived files (PIV fields), ('on' by default) |
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59 | 'RootFile';'on';... %root input file name ('on' by default) |
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60 | 'FileExt';'on';... %inputf file extension ('on' by default) |
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61 | 'NomType';'on';...%type of file indexing ('on' by default) |
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62 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
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63 | %'VelTypeMenu';'on';...% menu for selecting the velocity type (civ1,..)('off' by default) |
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64 | %'FieldMenu';'on';...% menu for selecting the velocity field (s) in the input file ('off' by default) |
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65 | %'VelTypeMenu_1';'on';...% menu for selecting the velocity type (civ1,..)('off' by default) |
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66 | %'FieldMenu_1';'on';...% menu for selecting the velocity field (s) in the input file ('off' by default) |
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67 | %'CoordType';...%can use a transform function |
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68 | %'GetObject';...;%can use projection object |
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69 | %'GetMask';...;%can use mask option |
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70 | %'PARAMETER';'NbSliding';... |
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71 | %'PARAMETER';'VolumeScan';... |
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72 | %'PARAMETER';'RankBrightness';... |
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73 | ''}; |
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74 | return %exit the function |
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75 | end |
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76 | |
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77 | %---------------------------------------------------------------- |
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78 | %% initiate the waitbar |
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79 | hseries=guidata(Series.hseries);%handles of the GUI series |
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80 | WaitbarPos=get(hseries.waitbar_frame,'Position'); |
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81 | %----------------------------------------------------------------- |
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82 | if iscell(Series.RootPath) |
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83 | msgbox_uvmat('ERROR','This function use only one input image series') |
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84 | return |
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85 | end |
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86 | |
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87 | %% determine input image type |
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88 | FileType=[];%default |
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89 | MovieObject=[]; |
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90 | FileExt=Series.FileExt; |
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91 | |
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92 | if isequal(lower(FileExt),'.avi') |
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93 | hhh=which('mmreader'); |
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94 | if ~isequal(hhh,'')&& mmreader.isPlatformSupported() |
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95 | MovieObject=mmreader(fullfile(RootPath,[RootFile FileExt])); |
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96 | FileType='movie'; |
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97 | else |
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98 | FileType='avi'; |
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99 | end |
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100 | elseif isequal(lower(FileExt),'.vol') |
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101 | FileType='vol'; |
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102 | else |
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103 | form=imformats(FileExt(2:end)); |
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104 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
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105 | if isequal(Series.NomType,'*'); |
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106 | FileType='multimage'; |
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107 | else |
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108 | FileType='image'; |
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109 | end |
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110 | end |
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111 | end |
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112 | if isempty(FileType) |
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113 | msgbox_uvmat('ERROR',['invalid file extension ' FileExt ': this function only accepts image or movie input']) |
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114 | return |
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115 | end |
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116 | |
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117 | nbslice_i=Series.NbSlice; %number of slices |
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118 | siz=size(num_i1); |
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119 | 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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120 | |
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121 | filebase=fullfile(Series.RootPath,Series.RootFile); |
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122 | dir_images=Series.RootPath; |
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123 | nom_type=Series.NomType; |
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124 | |
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125 | %% create dir of the new image |
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126 | % [dir_images,namebase]=fileparts(filebase); |
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127 | term='_background'; |
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128 | |
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129 | [pp,subdir_ima]=fileparts(Series.RootPath); |
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130 | try |
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131 | mkdir([dir_images term]); |
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132 | catch ME |
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133 | msgbox_uvmat('ERROR',ME.message); |
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134 | return |
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135 | end |
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136 | [xx,msg2] = fileattrib([dir_images term],'+w','g'); %yield writing access (+w) to user group (g) |
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137 | if ~strcmp(msg2,'') |
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138 | msgbox_uvmat('ERROR',['pb of permission for ' subdir_ima term ': ' msg2])%error message for directory creation |
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139 | return |
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140 | end |
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141 | filebase_b=fullfile([dir_images term],Series.RootFile); |
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142 | |
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143 | %% set processing parameters |
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144 | prompt = {'The number of positions (laser slices)';'volume scan mode (Yes/No)';... |
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145 | 'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'}; |
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146 | dlg_title = ['get (slice by slice) a background , result in subdir ' subdir_ima term]; |
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147 | num_lines= 3; |
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148 | def = {'1';'No';'0.1'}; |
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149 | answer = inputdlg(prompt,dlg_title,num_lines,def); |
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150 | vol_test=answer{2}; |
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151 | if isequal(vol_test,'Yes') |
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152 | nbfield2=1;%case of volume: no consecutive series at a given level |
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153 | nbslice_i=siz(1);%number of slices |
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154 | else |
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155 | nbfield2=siz(1); %nb of consecutive images at each level(burst) |
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156 | % if siz(2)>1 |
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157 | % nbslice_i=str2num(answer{1})/(num_i1(1,2)-num_i1(1,1));% number of slices |
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158 | % else |
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159 | nbslice_i=1; |
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160 | % end |
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161 | % if ~isequal(floor(nbslice_i),nbslice_i) |
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162 | % msgbox_uvmat('ERROR','the number of slices must be a multiple of the i increment') |
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163 | % return |
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164 | % end |
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165 | end |
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166 | lengthtot=siz(1)*siz(2); |
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167 | nbfield=floor(lengthtot/(nbfield2*nbslice_i));%total number of i indexes (adjusted to an integer number of slices) |
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168 | nbfield_slice=nbfield*nbfield2;% number of fields per slic |
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169 | rank=floor(str2num(answer{3})*nbfield_slice); |
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170 | if rank==0 |
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171 | rank=1;%rank selected in the sorted image series |
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172 | end |
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173 | |
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174 | %% prealocate memory for the background |
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175 | first_image=name_generator(filebase,num_i1(1),num_j1(1),Series.FileExt,Series.NomType); |
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176 | Afirst=read_image(first_image,FileType,num_i1(1),MovieObject); |
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177 | [npy,npx]=size(Afirst); |
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178 | try |
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179 | Ak=zeros(npy,npx,nbfield_slice,'uint16'); %prealocate memory |
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180 | catch ME |
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181 | msgbox_uvmat('ERROR',ME.message) |
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182 | return |
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183 | end |
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184 | |
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185 | |
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186 | %MAIN LOOP ON SLICES |
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187 | % |
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188 | % nbfield_slice |
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189 | % nbslice_i |
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190 | % for islice=1:nbslice_i |
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191 | % %% select the series of image indices at the level islice |
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192 | % for ifield=1:nbfield |
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193 | % for iburst=1:nbfield2 |
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194 | % indselect(iburst,ifield)=((ifield-1)*nbslice_i+(islice-1))*nbfield2+iburst; |
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195 | % end |
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196 | % end |
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197 | % |
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198 | %% read the first series of nbaver_ima images and sort by luminosity at each pixel |
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199 | for ifile = 1:nbfield_slice |
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200 | % ifile=indselect(ifield); |
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201 | filename=name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt,Series.NomType) |
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202 | try |
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203 | Aread=read_image(filename,FileType,num_i1(ifile),MovieObject); |
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204 | catch ME |
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205 | msgbox_uvmat('ERROR',ME.message) |
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206 | return |
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207 | end |
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208 | Ak(:,:,ifile)=Aread; |
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209 | %finish the waitbar |
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210 | update_waitbar(hseries.waitbar,WaitbarPos,1) |
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211 | end |
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212 | Ak=sort(Ak,3); |
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213 | C=Ak(:,:,rank); |
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214 | [newname]=... |
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215 | name_generator(filebase_b,num_i1(1),num_j1(1),'.png','none') % makes the new file name |
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216 | imwrite(C,newname,'BitDepth',16); % save the new image |
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217 | % end |
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218 | |
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219 | |
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220 | |
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221 | |
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222 | %------------------------------------------------------------------------ |
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223 | %--read images and convert them to the uint16 format used for PIV |
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224 | function A=read_image(filename,type_ima,num,MovieObject) |
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225 | %------------------------------------------------------------------------ |
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226 | %num is the view number needed for an avi movie |
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227 | switch type_ima |
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228 | case 'movie' |
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229 | A=read(MovieObject,num); |
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230 | case 'avi' |
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231 | mov=aviread(filename,num); |
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232 | A=frame2im(mov(1)); |
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233 | case 'multimage' |
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234 | A=imread(filename,num); |
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235 | case 'image' |
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236 | A=imread(filename); |
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237 | end |
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238 | siz=size(A); |
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239 | if length(siz)==3;%color images |
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240 | A=sum(double(A),3); |
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241 | end |
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242 | |
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