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 | function ParamOut=sub_background (Param) |
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54 | |
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55 | %%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% |
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56 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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57 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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58 | ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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59 | ParamOut.NbSlice='on'; %nbre of slices ('off' by default) |
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60 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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61 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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62 | ParamOut.FieldTransform = 'off';%can use a transform function |
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63 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', |
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64 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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65 | ParamOut.OutputDirExt='.sback';%set the output dir extension |
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66 | 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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67 | |
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68 | %% root input file(s) and type |
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69 | % check the existence of the first file in the series |
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70 | first_j=[]; |
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71 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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72 | last_j=[]; |
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73 | if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end |
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74 | PairString=''; |
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75 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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76 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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77 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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78 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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79 | if ~exist(FirstFileName,'file') |
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80 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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81 | else |
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82 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); |
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83 | LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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84 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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85 | if ~exist(FirstFileName,'file') |
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86 | msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) |
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87 | end |
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88 | end |
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89 | |
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90 | %% check the validity of input file types |
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91 | ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images) |
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92 | FileType=get_file_type(FirstFileName); |
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93 | CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions), 1));% =1 for images |
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94 | if ~CheckImage |
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95 | msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not an image']) |
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96 | return |
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97 | end |
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98 | |
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99 | %% numbers of fields |
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100 | NbSlice=1;%default |
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101 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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102 | NbSlice=Param.IndexRange.NbSlice; |
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103 | end |
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104 | incr_j=1;%default |
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105 | if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j) |
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106 | incr_j=Param.IndexRange.incr_j; |
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107 | end |
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108 | if isempty(first_j)||isempty(last_j) |
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109 | nbfield_j=1; |
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110 | else |
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111 | nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices) |
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112 | end |
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113 | incr_i=1;%default |
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114 | first_i=1;last_i=1;incr_i;%default |
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115 | if isfield(Param.IndexRange,'first_i'); last_i=Param.IndexRange.first_i; end |
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116 | if isfield(Param.IndexRange,'last_i'); last_i=Param.IndexRange.last_j; end |
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117 | if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i) |
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118 | incr_i=Param.IndexRange.incr_i; |
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119 | end |
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120 | nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices) |
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121 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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122 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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123 | |
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124 | %% setting of parameters specific to sub_background |
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125 | 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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126 | if nbfield_i~=1 |
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127 | nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background, |
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128 | if isequal(floor(nbaver/2),nbaver) |
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129 | nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined) |
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130 | end |
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131 | nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts |
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132 | end |
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133 | |
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134 | prompt = {'volume scan mode (Yes/No)';'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';... |
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135 | 'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'}; |
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136 | dlg_title = 'get (slice by slice) a sliding background and substract to each image'; |
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137 | num_lines= 3; |
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138 | def = { 'No';num2str(nbaver_init);'0.1'}; |
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139 | answer = inputdlg(prompt,dlg_title,num_lines,def); |
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140 | |
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141 | %check input consistency |
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142 | if strcmp(answer{1},'No') && ~isequal(NbSlice,1) |
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143 | check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice) ' slices']); |
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144 | if ~strcmp(check,'Yes') |
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145 | return |
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146 | end |
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147 | end |
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148 | if strcmp(answer{1},'Yes') |
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149 | step=1; |
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150 | else |
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151 | step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst |
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152 | end |
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153 | nbaver_ima=str2num(answer{2});%number of images for the sliding background |
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154 | nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background |
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155 | if isequal(floor(nbaver/2),nbaver) |
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156 | nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) |
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157 | end |
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158 | nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver |
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159 | ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes'); |
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160 | ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima; |
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161 | ParamOut.ActionInput.BrightnessRankThreshold=str2num(answer{3}); |
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162 | |
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163 | % apply the image rescaling function 'level' (avoid the blinking effects of bright particles) |
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164 | answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background'); |
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165 | ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes'); |
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166 | return |
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167 | end |
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168 | %%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% |
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169 | |
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170 | %% read input parameters from an xml file if input is a file name (batch mode) |
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171 | checkrun=1; |
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172 | if ischar(Param) |
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173 | Param=xml2struct(Param);% read Param as input file (batch case) |
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174 | checkrun=0; |
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175 | end |
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176 | hseries=findobj(allchild(0),'Tag','series'); |
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177 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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178 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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179 | |
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180 | %% input preparation |
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181 | nbaver_ima=Param.ActionInput.SlidingSequenceLength; |
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182 | NbSlice=Param.IndexRange.NbSlice; |
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183 | if ~isequal(NbSlice,1) |
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184 | display(['multi-level splitting into ' num2str(NbSlice) ' slices']); |
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185 | end |
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186 | RootPath=Param.InputTable(:,1); |
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187 | RootFile=Param.InputTable(:,3); |
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188 | SubDir=Param.InputTable(:,2); |
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189 | NomType=Param.InputTable(:,4); |
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190 | FileExt=Param.InputTable(:,5); |
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191 | hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); |
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192 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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193 | if ~isempty(hdisp),delete(hdisp),end; |
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194 | %%%%%%%%%%%% |
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195 | % The cell array filecell is the list of input file names, while |
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196 | % filecell{iview,fileindex}: |
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197 | % iview: line in the table corresponding to a given file series |
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198 | % fileindex: file index within the file series, |
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199 | % 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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200 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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201 | %%%%%%%%%%%% |
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202 | [FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); |
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203 | if ~isempty(j1_series{1}) |
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204 | frame_index{1}=j1_series{1}; |
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205 | else |
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206 | frame_index{1}=i1_series{1}; |
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207 | end |
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208 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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209 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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210 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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211 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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212 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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213 | |
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214 | %% output |
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215 | FileExtOut='.png'; % write result as .png images for image inputs |
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216 | if strcmp(lower(NomType{1}(end)),'a') |
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217 | NomTypeOut=NomType{1};%case of letter appendix |
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218 | elseif isempty(j1_series) |
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219 | NomTypeOut='_1'; |
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220 | else |
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221 | NomTypeOut='_1_1';% caseof purely numerical indexing |
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222 | end |
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223 | |
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224 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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225 | |
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226 | if isequal(Param.ActionInput.CheckVolume,1) |
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227 | step=1; |
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228 | else |
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229 | step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst |
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230 | end |
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231 | nbaver_ima=Param.ActionInput.SlidingSequenceLength;%number of images for the sliding background |
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232 | nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background |
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233 | if isequal(floor(nbaver/2),nbaver) |
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234 | nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) |
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235 | end |
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236 | nbaver_ima=nbaver*step; |
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237 | if nbaver_ima > nbfield |
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238 | display('number of images in a slice smaller than the proposed number of images for the sliding average') |
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239 | return |
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240 | end |
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241 | |
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242 | % calculate absolute brightness rank |
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243 | rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima); |
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244 | if rank==0 |
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245 | rank=1;%rank selected in the sorted image series |
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246 | end |
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247 | |
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248 | %% prealocate memory for the sliding background |
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249 | try |
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250 | Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1)); |
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251 | [npy,npx,nbcolor]=size(Afirst);% the argument nbcolor is important to get npx right for color images |
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252 | if strcmp(class(Afirst),'uint8') % case of 8bit images |
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253 | Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory |
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254 | Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory |
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255 | else |
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256 | Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
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257 | Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
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258 | end |
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259 | catch ME |
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260 | msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message]) |
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261 | return |
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262 | end |
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263 | |
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264 | %% summary of the parameters: |
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265 | % nbfield : total number of images treated (in case of multislices the function sub_background is repeated for each slice) |
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266 | % step: shift at each step of the sliding background (corresponding to the nbre of images in a burst) |
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267 | % nbaver_ima: length of the sequence used for the sliding background |
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268 | |
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269 | % nbaver=nbaver_ima/step: nbaver_ima has been adjusted so that nbaver is an odd integer |
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270 | halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background |
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271 | |
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272 | %% select the series of image indices to process |
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273 | indselect=1:step:nbfield;% select file indices of the slice |
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274 | for ifield=1:step-1 |
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275 | indselect=[indselect;indselect(end,:)+1]; |
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276 | end |
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277 | |
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278 | %% read the first series of nbaver_ima images and sort by luminosity at each pixel |
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279 | for ifield = 1:nbaver_ima |
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280 | ifile=indselect(ifield); |
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281 | filename=filecell{1,ifile}; |
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282 | Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); |
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283 | if ndims(Aread)==3;%color images |
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284 | Aread=sum(double(Aread),3);% take the sum of color components |
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285 | end |
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286 | Ak(:,:,ifield)=Aread; |
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287 | end |
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288 | Asort=sort(Ak,3);%sort the luminosity of images at each point |
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289 | B=Asort(:,:,rank);%background image |
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290 | |
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291 | %% substract the first background image to the first images |
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292 | display( 'first background image will be substracted') |
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293 | for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image |
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294 | Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image |
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295 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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296 | ifile=indselect(ifield); |
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297 | if ~isempty(j1_series{1}) |
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298 | j1=j1_series{1}(ifile); |
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299 | end |
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300 | newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
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301 | |
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302 | %write result file |
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303 | if Param.ActionInput.CheckLevelTransform |
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304 | C=levels(Acor); |
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305 | imwrite(C,newname,'BitDepth',8); % save the new image |
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306 | else |
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307 | if isequal(FileInfo{1}.BitDepth,16) |
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308 | C=uint16(Acor); |
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309 | imwrite(C,newname,'BitDepth',16); % save the new image |
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310 | else |
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311 | C=uint8(Acor); |
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312 | imwrite(C,newname,'BitDepth',8); % save the new image |
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313 | end |
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314 | end |
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315 | display([newname ' written']) |
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316 | end |
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317 | |
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318 | %% repeat the operation on a sliding series of images |
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319 | display('sliding background image will be substracted') |
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320 | if nbfield_i > nbaver_ima |
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321 | for ifield = step*(halfnbaver+1):step:nbfield_i-step*(halfnbaver+1)% ifield +iburst=index of the current processed image |
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322 | update_waitbar(WaitbarHandle,ifield/nbfield_i) |
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323 | if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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324 | disp('program stopped by user') |
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325 | return |
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326 | end |
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327 | Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step) |
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328 | %incorporate next burst in the current image series |
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329 | for iburst=1:step |
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330 | ifile=indselect(ifield+iburst+step*halfnbaver); |
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331 | filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1_series{1}(ifile)); |
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332 | Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile)); |
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333 | if ndims(Aread)==3;%color images |
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334 | Aread=sum(double(Aread),3);% take the sum of color components |
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335 | end |
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336 | Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image |
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337 | end |
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338 | Asort=sort(Ak,3);%sort the new current image series by luminosity |
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339 | B=Asort(:,:,rank);%current background image |
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340 | %substract the background for the current burst |
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341 | for iburst=1:step |
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342 | 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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343 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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344 | ifile=indselect(ifield+iburst); |
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345 | if ~isempty(j1_series{1}) |
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346 | j1=j1_series{1}(ifile); |
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347 | end |
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348 | newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
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349 | %write result file |
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350 | if Param.ActionInput.CheckLevelTransform |
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351 | C=levels(Acor); |
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352 | imwrite(C,newname,'BitDepth',8); % save the new image |
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353 | else |
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354 | if isequal(FileInfo{1}.BitDepth,16) |
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355 | C=uint16(Acor); |
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356 | imwrite(C,newname,'BitDepth',16); % save the new image |
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357 | else |
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358 | C=uint8(Acor); |
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359 | imwrite(C,newname,'BitDepth',8); % save the new image |
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360 | end |
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361 | end |
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362 | display([newname ' written']) |
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363 | end |
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364 | end |
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365 | end |
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366 | |
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367 | %% substract the background from the last images |
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368 | display('last background image will be substracted') |
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369 | for ifield=nbfield_i-step*halfnbaver+1:nbfield_i |
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370 | Acor=double(Ak(:,:,ifield-nbfield_i+step*(2*halfnbaver+1)))-double(B); |
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371 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
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372 | ifile=indselect(ifield); |
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373 | if ~isempty(j1_series{1}) |
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374 | j1=j1_series{1}(ifile); |
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375 | end |
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376 | newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
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377 | %write result file |
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378 | if Param.ActionInput.CheckLevelTransform |
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379 | C=levels(Acor); |
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380 | imwrite(C,newname,'BitDepth',8); % save the new image |
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381 | else |
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382 | if isequal(FileInfo{1}.BitDepth,16) |
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383 | C=uint16(Acor); |
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384 | imwrite(C,newname,'BitDepth',16); % save the new image |
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385 | else |
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386 | C=uint8(Acor); |
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387 | imwrite(C,newname,'BitDepth',8); % save the new image |
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388 | end |
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389 | end |
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390 | display([newname ' written']) |
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391 | end |
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392 | |
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393 | |
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394 | |
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395 | function C=levels(A) |
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396 | %whos A; |
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397 | B=double(A(:,:,1)); |
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398 | windowsize=round(min(size(B,1),size(B,2))/20); |
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399 | windowsize=floor(windowsize/2)*2+1; |
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400 | ix=1/2-windowsize/2:-1/2+windowsize/2;% |
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401 | %del=np/3; |
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402 | %fct=exp(-(ix/del).^2); |
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403 | fct2=cos(ix/(windowsize-1)/2*pi/2); |
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404 | %Mfiltre=(ones(5,5)/5^2); |
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405 | %Mfiltre=fct2'; |
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406 | Mfiltre=fct2'*fct2; |
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407 | Mfiltre=Mfiltre/(sum(sum(Mfiltre))); |
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408 | |
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409 | C=filter2(Mfiltre,B); |
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410 | C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize); |
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411 | C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize); |
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412 | C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:); |
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413 | C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:); |
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414 | C=tanh(B./(2*C)); |
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415 | [n,c]=hist(reshape(C,1,[]),100); |
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416 | % figure;plot(c,n); |
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417 | |
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418 | [m,i]=max(n); |
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419 | c_max=c(i); |
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420 | [dummy,index]=sort(abs(c-c(i))); |
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421 | n=n(index); |
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422 | c=c(index); |
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423 | i_select = find(cumsum(n)<0.95*sum(n)); |
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424 | if isempty(i_select) |
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425 | i_select = 1:length(c); |
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426 | end |
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427 | c_select=c(i_select); |
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428 | n_select=n(i_select); |
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429 | cmin=min(c_select); |
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430 | cmax=max(c_select); |
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431 | C=(C-cmin)/(cmax-cmin)*256; |
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432 | C=uint8(C); |
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