[1097] | 1 | %'bed_scan': get the bed shape from laser ipact |
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| 2 | |
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| 3 | %------------------------------------------------------------------------ |
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| 4 | % function GUI_input=bed_scan(Param) |
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| 5 | % |
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| 6 | %------------------------------------------------------------------------ |
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| 7 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 8 | % |
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| 9 | %OUTPUT |
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| 10 | % ParamOut: sets options in the GUI series.fig needed for the function |
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| 11 | % |
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| 12 | %INPUT: |
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| 13 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 14 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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| 15 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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| 16 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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| 17 | % |
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| 18 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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| 19 | % see the current structure Param) |
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| 20 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 21 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 22 | % .OutputSubDir: name of the subdirectory for data outputs |
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| 23 | % .OutputDirExt: directory extension for data outputs |
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| 24 | % .Action: .ActionName: name of the current activated function |
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| 25 | % .ActionPath: path of the current activated function |
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| 26 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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| 27 | % .RUN =0 for GUI input, =1 for function activation |
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| 28 | % .RunMode='local','background', 'cluster': type of function use |
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| 29 | % |
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| 30 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 31 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 32 | % .TransformPath: path of the selected transform function |
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| 33 | % .InputFields: sub structure describing the input fields withfields |
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| 34 | % .FieldName: name(s) of the field |
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| 35 | % .VelType: velocity type |
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| 36 | % .FieldName_1: name of the second field in case of two input series |
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| 37 | % .VelType_1: velocity type of the second field in case of two input series |
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| 38 | % .Coord_y: name of y coordinate variable |
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| 39 | % .Coord_x: name of x coordinate variable |
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| 40 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 41 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 42 | |
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| 43 | %======================================================================= |
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[1107] | 44 | % Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[1097] | 45 | % http://www.legi.grenoble-inp.fr |
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| 46 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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| 47 | % |
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| 48 | % This file is part of the toolbox UVMAT. |
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| 49 | % |
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| 50 | % UVMAT is free software; you can redistribute it and/or modify |
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| 51 | % it under the terms of the GNU General Public License as published |
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[1098] | 52 | % by the Free Software Foundation; either version 2 of the license,series |
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[1097] | 53 | % or (at your option) any later version. |
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| 54 | % |
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| 55 | % UVMAT is distributed in the hope that it will be useful, |
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| 56 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 57 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 58 | % GNU General Public License (see LICENSE.txt) for more details. |
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| 59 | %======================================================================= |
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| 60 | |
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| 61 | function ParamOut=sub_background_special (Param) |
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| 62 | |
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| 63 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed |
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| 64 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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| 65 | ParamOut.NbViewMax=1;% max nbre of input file series (default , no limitation) |
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| 66 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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| 67 | ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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[1098] | 68 | ParamOut.NbSlice='on'; %nbre of slices ('off' by default) |
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[1097] | 69 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 70 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 71 | ParamOut.FieldTransform = 'off';%can use a transform function |
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| 72 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', |
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| 73 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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| 74 | ParamOut.OutputDirExt='.sback';%set the output dir extension |
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| 75 | 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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| 76 | %check the type of the existence and type of the first input file: |
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| 77 | return |
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| 78 | end |
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| 79 | |
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| 80 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 81 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 82 | ParamOut=[]; |
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| 83 | RUNHandle=[]; |
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| 84 | WaitbarHandle=[]; |
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| 85 | checkrun=1; |
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| 86 | if ischar(Param)% case of batch: Param is the name of the xml file containing the input parameters |
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| 87 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 88 | checkrun=0; |
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| 89 | else% interactive mode in Matlab |
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| 90 | hseries=findobj(allchild(0),'Tag','series'); |
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| 91 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 92 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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| 93 | end |
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| 94 | %% estimate the position of bottom and mask for each Z Index |
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[1098] | 95 | NbSlice=Param.IndexRange.NbSlice; |
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| 96 | switch NbSlice |
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| 97 | case 11 |
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| 98 | BottomIndex=[1900 1800 1700 1650 1650 1600 1600 1600 1600 1600 1600]; |
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| 99 | case 4 |
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| 100 | BottomIndex=[1950 1850 1740 1700]; |
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| 101 | end |
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[1097] | 102 | MaxIndex=BottomIndex+100; |
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| 103 | MinIndex=BottomIndex-100; |
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[1098] | 104 | |
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[1097] | 105 | maskindex=[665 1080];% range of x index perturbed by shadows |
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| 106 | Bfilter=ones(1,20)/20; |
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| 107 | %% root input file names and nomenclature type (cell arrays with one element) |
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[1124] | 108 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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[1097] | 109 | nbj=numel(Param.IndexRange.first_i:Param.IndexRange.last_i); |
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| 110 | for i_ind=Param.IndexRange.first_i:Param.IndexRange.last_i |
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| 111 | ZIndex=mod(i_ind-1,NbSlice)+1; |
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| 112 | for j_ind=Param.IndexRange.first_j:Param.IndexRange.last_j |
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| 113 | % read the current image |
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| 114 | InputFile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},Param.InputTable{1,4},i_ind,i_ind,j_ind); |
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| 115 | A=imread(InputFile); |
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| 116 | % get the bottom as the max of luminosity along vertical lines |
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| 117 | IndexMax=ones(1,size(A,2));%initiate the index position of the bottom |
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| 118 | if j_ind==Param.IndexRange.first_j |
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| 119 | indexMax_j=ones(nbj,size(A,2));%initiate the matrix of index position of the bottom |
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| 120 | end |
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| 121 | for icolumn=1:maskindex(1) |
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| 122 | [M,IndexMax(icolumn)] = max(A(MinIndex(ZIndex)+1:MaxIndex(ZIndex),icolumn),[],1); |
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| 123 | end |
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| 124 | [M,IndexMax(maskindex(2))] = max(A(MinIndex(ZIndex)+1:MaxIndex(ZIndex),maskindex(2)),[],1); |
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| 125 | for icolumn=maskindex(1)+1:maskindex(2)-1 % linear interpolation in the masked region |
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| 126 | IndexMax(icolumn)= IndexMax(maskindex(1))*(maskindex(2)-icolumn)+IndexMax(maskindex(2))*(icolumn-maskindex(1)); |
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| 127 | IndexMax(icolumn)=IndexMax(icolumn)/(maskindex(2)-maskindex(1)); |
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| 128 | end |
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| 129 | for icolumn=maskindex(2)+1:size(A,2) |
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| 130 | [M,IndexMax(icolumn)] = max(A(MinIndex(ZIndex)+1:MaxIndex(ZIndex),icolumn),[],1); |
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| 131 | end |
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| 132 | IndexFilt=filter(Bfilter,1,IndexMax);% smoothed IndexMax |
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| 133 | peakdetect=find(abs(IndexFilt-IndexMax)>5);% detect strong departures from the filtered values |
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| 134 | IndexMax(peakdetect)=IndexFilt(peakdetect);%replace the peaks by the filtered values |
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| 135 | IndexMax_j(j_ind,:)=round(filter(Bfilter,1,IndexMax));%filter again and take the closest integer |
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| 136 | % get the background image as the min at each point in the j series |
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| 137 | if j_ind==Param.IndexRange.first_j |
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| 138 | Amin=A; |
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| 139 | else |
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| 140 | Amin=min(Amin,A); |
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| 141 | end |
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| 142 | end |
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| 143 | |
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| 144 | for j_ind=Param.IndexRange.first_j:Param.IndexRange.last_j |
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| 145 | InputFile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},Param.InputTable{1,4},i_ind,i_ind,j_ind); |
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| 146 | A=imread(InputFile); |
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| 147 | A=A-Amin; |
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| 148 | for icolumn=1:size(A,2) |
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| 149 | A(MinIndex(ZIndex)+IndexMax_j(j_ind,icolumn):end,icolumn)=0; |
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| 150 | end |
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| 151 | OutputFile=fullfile_uvmat(Param.InputTable{1,1},OutputDir,Param.InputTable{1,3},Param.InputTable{1,5},Param.InputTable{1,4},i_ind,i_ind,j_ind); |
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| 152 | imwrite(A,OutputFile) |
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| 153 | disp([OutputFile ' written']) |
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| 154 | end |
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| 155 | end |
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