[810] | 1 | %======================================================================= |
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[977] | 2 | % Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[810] | 3 | % http://www.legi.grenoble-inp.fr |
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| 4 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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| 5 | % |
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| 6 | % This file is part of the toolbox UVMAT. |
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| 7 | % |
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| 8 | % UVMAT is free software; you can redistribute it and/or modify |
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| 9 | % it under the terms of the GNU General Public License as published |
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| 10 | % by the Free Software Foundation; either version 2 of the license, |
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| 11 | % or (at your option) any later version. |
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| 12 | % |
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| 13 | % UVMAT is distributed in the hope that it will be useful, |
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| 14 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 15 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 16 | % GNU General Public License (see LICENSE.txt) for more details. |
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| 17 | %======================================================================= |
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| 18 | |
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[779] | 19 | function ParamOut=beam_forming(Param) |
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| 20 | |
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| 21 | %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed |
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| 22 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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| 23 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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[781] | 24 | ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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[779] | 25 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default) |
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| 26 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 27 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 28 | ParamOut.FieldTransform = 'off';%can use a transform function |
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| 29 | %ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) |
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| 30 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', |
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| 31 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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[781] | 32 | index=msgbox_uvmat('INPUT_TXT','index of the series to process (1 to 5)');%choose the i index of the dat files |
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| 33 | ParamOut.OutputDirExt=['.p_formed_' index];%set the output dir extension |
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| 34 | hseries=findobj(allchild(0),'Tag','series'); |
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| 35 | hhseries=guidata(hseries); |
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| 36 | set(hhseries.num_last_i,'String',index) |
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| 37 | set(hhseries.num_first_i,'String',index) |
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[779] | 38 | 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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| 39 | %check the input files |
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| 40 | first_j=[]; |
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| 41 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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| 42 | PairString=''; |
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| 43 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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| 44 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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| 45 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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| 46 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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| 47 | if ~exist(FirstFileName,'file') |
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| 48 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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| 49 | end |
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| 50 | return |
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| 51 | end |
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| 52 | |
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| 53 | ParamOut=[]; %default output |
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[781] | 54 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 55 | checkrun=1; |
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| 56 | if ischar(Param) |
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| 57 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 58 | checkrun=0; |
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| 59 | end |
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[779] | 60 | hseries=findobj(allchild(0),'Tag','series'); |
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| 61 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 62 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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| 63 | |
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| 64 | %% define the directory for result file (with path=RootPath{1}) |
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| 65 | OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files |
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| 66 | if ~isfield(Param,'InputFields') |
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| 67 | Param.InputFields.FieldName=''; |
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| 68 | end |
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| 69 | |
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| 70 | %% root input file type |
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| 71 | RootPath=Param.InputTable{1,1}; |
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| 72 | RootFile=Param.InputTable{1,3}; |
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| 73 | SubDir=Param.InputTable{1,2}; |
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| 74 | NomType=Param.InputTable{1,4}; |
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| 75 | FileExt=Param.InputTable{1,5}; |
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| 76 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 77 | %%%%%%%%%%%% |
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| 78 | % The cell array filecell is the list of input file names, while |
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| 79 | % filecell{iview,fileindex}: |
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| 80 | % iview: line in the table corresponding to a given file series |
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| 81 | % fileindex: file index within the file series, |
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| 82 | % 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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| 83 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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| 84 | %%%%%%%%%%%% |
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| 85 | % NbSlice=1;%default |
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| 86 | % if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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| 87 | % NbSlice=Param.IndexRange.NbSlice; |
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| 88 | % end |
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| 89 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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| 90 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 91 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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| 92 | NbField=NbField_j*NbField_i; %total number of fields |
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| 93 | |
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| 94 | %% determine the file type on each line from the first input file |
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[984] | 95 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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[779] | 96 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 97 | for iview=1:NbView |
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| 98 | if ~exist(filecell{iview,1}','file') |
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| 99 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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| 100 | return |
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| 101 | end |
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[784] | 102 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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[783] | 103 | FileType{iview}=FileInfo{iview}.FileType; |
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[779] | 104 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 105 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 106 | if ~isempty(j1_series{iview}) |
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| 107 | frame_index{iview}=j1_series{iview}; |
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| 108 | else |
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| 109 | frame_index{iview}=i1_series{iview}; |
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| 110 | end |
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| 111 | end |
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| 112 | |
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| 113 | % clear all |
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| 114 | % close all |
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| 115 | % read_data=1; |
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[781] | 116 | affichage=0; |
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[779] | 117 | % soustraction=0; |
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| 118 | |
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| 119 | %%%%%% Prepare output |
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| 120 | load (fullfile(RootPath,SubDir,[RootFile '.mat'])) |
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[781] | 121 | Data.ListGlobalAttribute={'CoordUnit'}; %%TODO: add also time, how to get it ????? |
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| 122 | Data.CoordUnit='pixel'; |
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[782] | 123 | Data.ListVarName={'Coord_x','Coord_y','A'}; |
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| 124 | Data.VarDimName={'Coord_x','Coord_y',{'Coord_y','Coord_x'}}; |
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[781] | 125 | %Data.Coord_x=5*(nbvoie_reception-0.5)/numel(nbvoie_reception); % totql length of e |
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[782] | 126 | Data.Coord_x=1:65; |
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[781] | 127 | %Data.Coord_z=(1:A)/133 ;% to check from input parameter .... |
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[782] | 128 | Data.Coord_y=1:332; |
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[779] | 129 | %%%%%% |
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| 130 | % |
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| 131 | % while test_fin_fichier>0 |
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| 132 | % if read_data==1 |
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[780] | 133 | %directory='manip_lgit';%%%%%%%%%%%%%%%%% |
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| 134 | %name='test';%%%%%%%%%%%%%%%%% |
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[779] | 135 | % number=2; |
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[781] | 136 | number=str2num(Param.OutputDirExt(11:end));%extract the subsequence index (from 1 to 5) |
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| 137 | numero_tir_fin_old=1%%%%%%% =0 ????? |
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| 138 | pas_fichier=20;% %20;% nbre of successive shots to read (to account for computer memory limit) |
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| 139 | Nmoy=800; %%%%% value 20 FOR TEST : to shift to VALUE 8000 set by the .mat file |
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[779] | 140 | |
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[780] | 141 | test_fin_fichier=1;% test to stop input file reading |
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| 142 | while test_fin_fichier>0 |
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| 143 | numero_tir_debut=1; |
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[781] | 144 | numero_tir_fin=numero_tir_fin_old+pas_fichier-1; |
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[779] | 145 | |
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[780] | 146 | % eval(['load ' directory '\' name '.mat']) |
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| 147 | matrice_finale=zeros(A,length(nbvoie_reception),numero_tir_fin);%A=nbre of times (coord z)=2650, numero_tir_fin=time index |
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| 148 | time=(b/rsf+[0:A-1]/rsf); %b=250, rsf=10, |
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| 149 | freq1=0.5;freq2=1.5; |
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| 150 | [BB AA]=butter(4,[freq1 freq2]/rsf*2); |
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[779] | 151 | |
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[780] | 152 | for ii=1:length(nbvoie_reception)%=64 |
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| 153 | %eval(['fid=fopen(''E:\ManipLGITLecoeur\' directory '\' name '_' num2str(number) '_' num2str(nbvoie_reception(ii)) '.dat'',''r'');']); |
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[781] | 154 | filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,number,[],ii); % input file name |
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[780] | 155 | fid=fopen(filename); |
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| 156 | toto=zeros(Nsequence*A*numero_tir_fin+31,1);% Nsequence=1 |
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[781] | 157 | toto=fread(fid,numero_tir_fin*A*Nsequence+31,'int16','ieee-le') ;% why shift by 31 ????? |
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[780] | 158 | toto=double(bitxor(uint16(toto),uint16(2048))); |
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| 159 | toto(1:31)=[];toto(numero_tir_fin*A*Nsequence)=mean(toto); |
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| 160 | fclose(fid); |
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[779] | 161 | |
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[780] | 162 | tata=reshape(toto-2048,A,numero_tir_fin); |
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| 163 | matrice_finale(:,ii,:)=reshape(tata,[A,1,numero_tir_fin]); |
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| 164 | clear toto tata |
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[779] | 165 | end |
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| 166 | |
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[781] | 167 | % matrice_finale(:,:,numero_tir_debut:numero_tir_fin_old)=[];%%%%%%% first field removed (when numero_tir_fin_old=1) ????? |
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| 168 | matrice_finale(:,:,numero_tir_debut:numero_tir_fin_old-1)=[];%%%%%%% |
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| 169 | % numero_tir_fin=numero_tir_fin-1; ????? |
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| 170 | matrice_finale=reshape(filtfilt(BB,AA,matrice_finale(:,:)),size(matrice_finale));% low pass filtered input signal,along first (time) index? |
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[780] | 171 | |
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| 172 | % if soustraction==1 |
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| 173 | % eval(['load moyenne_' name '_' num2str(number) '.mat matrice_finale_moy']) |
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| 174 | % for kk=1:size(matrice_finale,3) |
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| 175 | % matrice_finale(:,:,kk)=matrice_finale(:,:,kk)-matrice_finale_moy; |
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| 176 | % end |
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| 177 | % end |
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| 178 | %eval(['save matrice_finale_' num2str(numero_tir_fin_old) '_' num2str(numero_tir_fin) '.mat']) |
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| 179 | |
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| 180 | %%%%%%%%%%%%%%Imagerie |
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[781] | 181 | fe=rsf*1e6;% sampling frequency for receptor (in Hz) |
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[780] | 182 | cc=1475;%speed of sound |
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| 183 | hanning_window=25; |
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| 184 | hanning_vect=hanning(2*hanning_window+1); |
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| 185 | interval=[1:size(matrice_finale,1)]; |
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| 186 | freq=0:fe/length(interval):fe*(1-1/length(interval)); |
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| 187 | |
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| 188 | pas_reseau_z=0.75e-3;%0.75e-3 |
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| 189 | pas_reseau_r=0; |
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| 190 | voie_mean=length(nbvoie_reception)/2;%32; |
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| 191 | reseau_z=[0:length(nbvoie_reception)-1]*pas_reseau_z; |
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| 192 | reseau_z=reseau_z-reseau_z(voie_mean); |
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| 193 | reseau_r=[0:length(nbvoie_reception)-1]*pas_reseau_r; |
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| 194 | reseau_r=reseau_r-reseau_r(voie_mean); |
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| 195 | |
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| 196 | debut_r=(time(1)+20)*1e-6*cc/2; |
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| 197 | fin_r=(time(end)-20)*1e-6*cc/2; |
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| 198 | |
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| 199 | image_r=debut_r:.5e-3:fin_r; |
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| 200 | image_z=-24e-3:.75e-3:24e-3; |
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| 201 | |
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| 202 | image_fin=zeros(length(image_r),length(image_z),size(matrice_finale,3));%size=(332,65,pas_fichier) |
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| 203 | %image_fin_bis=zeros(length(image_r),length(image_z),size(matrice_finale,3)); |
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| 204 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 205 | |
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| 206 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 207 | for kk=1:size(matrice_finale,3) |
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[781] | 208 | disp(kk) |
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| 209 | signal=squeeze(matrice_finale(interval,:,kk)); |
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| 210 | tata_fft=fft(signal,[],1);%FFT of the time signal size=(2650,64) |
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| 211 | if kk==1 |
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[780] | 212 | matrice_freq_mean=mean(abs(fft(signal,[],1)),2); |
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| 213 | X=[freq1*1e6 freq2*1e6]; |
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| 214 | [I J]=find(freq>=X(1) & freq<=X(2)); |
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| 215 | int_freq=find(matrice_freq_mean(round(1:length(freq)/2))>max(matrice_freq_mean(round(1:length(freq)/2)))/2); |
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| 216 | bandwidth=freq(int_freq(end)-int_freq(1)); |
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| 217 | %clear matrice_freq_mean |
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| 218 | end |
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| 219 | |
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| 220 | for ii=1:length(image_r) |
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| 221 | for jj=1:length(image_z) |
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| 222 | |
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| 223 | delay=zeros(length(nbvoie_reception),1); |
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| 224 | delay=1/cc*sqrt((reseau_z-image_z(jj)).^2+(reseau_r-image_r(ii)).^2); |
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| 225 | |
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| 226 | [ind centre_z]=min(abs((reseau_z-image_z(jj)))); |
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| 227 | interval_utile=round(((delay(centre_z)+1/cc*abs(image_r(ii)))*fe)-(b+interval(1)-1)+round(length(motifbase)/2)+[-fe/bandwidth/2:fe/bandwidth/2]); |
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| 228 | delay=delay-delay(centre_z); |
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| 229 | |
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| 230 | hanning_vecteur=zeros(1,length(nbvoie_reception)); |
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| 231 | if centre_z>hanning_window & centre_z<(length(nbvoie_reception)-hanning_window) |
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| 232 | hanning_vecteur(centre_z+[-hanning_window:hanning_window])=hanning_vect; |
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| 233 | elseif centre_z<=hanning_window |
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| 234 | test=hanning_vect((centre_z+[-hanning_window:hanning_window])>=1); |
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| 235 | hanning_vecteur(1:length(test))=test; |
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| 236 | elseif centre_z>=(length(nbvoie_reception)-hanning_window) |
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| 237 | test=hanning_vect((centre_z+[-hanning_window:hanning_window])<=length(nbvoie_reception)); |
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| 238 | hanning_vecteur(length(nbvoie_reception)+[-length(test)+1:0])=test; |
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| 239 | end |
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| 240 | hanning_vecteur=hanning_vecteur/norm(hanning_vecteur); |
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| 241 | clear test; |
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| 242 | |
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| 243 | amplitude_weight=ones(size(signal,1),1)*hanning_vecteur; |
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| 244 | signal_new_rec=zeros(size(signal,1),length(nbvoie_reception)); |
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| 245 | |
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| 246 | tata=zeros(size(signal,1),size(signal,2)); |
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| 247 | tata(J,:)=tata_fft(J,:).*exp(1i*2*pi*(freq(J)'*delay)); |
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| 248 | signal_new_rec=2*real(ifft(tata,[],1)).*amplitude_weight; |
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| 249 | index_interval_utile=find(interval_utile>0 & interval_utile<size(signal,1)); |
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| 250 | toto=zeros(length(index_interval_utile),1); |
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| 251 | toto=mean(signal_new_rec(interval_utile(index_interval_utile),:),2); |
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| 252 | image_fin(ii,jj,kk)=sqrt(mean(toto.^2)); |
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| 253 | clear signal_bis interval_utile index_interval_utile hanning_vecteur |
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[779] | 254 | end |
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[780] | 255 | end |
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| 256 | end |
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| 257 | |
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| 258 | clear signal_new_em signal_new_rec m delay toto toto_bis tata tata_fft |
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| 259 | |
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| 260 | if affichage==1 |
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| 261 | for kk=1:size(image_fin,3) |
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[779] | 262 | |
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[780] | 263 | figure(1) |
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| 264 | imagesc(image_r*1e2,image_z*1e2,image_fin(:,:,kk)'/max(max(image_fin(:,:,kk)))'); |
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| 265 | title(['avec beamforming - energie max = ' num2str(max(max(image_fin(:,:,kk))))]) |
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| 266 | colorbar; |
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| 267 | xlabel('r (cm)');ylabel('z (cm)'); |
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| 268 | drawnow |
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| 269 | pause(.2); |
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[779] | 270 | end |
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| 271 | end |
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[780] | 272 | |
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| 273 | clear matrice_finale |
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| 274 | |
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| 275 | %%%%%%% TO ADAPT |
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| 276 | for iii=1:size(image_fin,3) |
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[781] | 277 | Data.A=image_fin(:,:,iii);% time lapse decreasesas z coordinate increases. |
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[780] | 278 | FileIndex=numero_tir_fin - pas_fichier+iii;%%%%%%TO CHECK!!!!! |
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| 279 | %%%%%%%%%% |
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| 280 | %eval(['save analyse_' name '_' num2str(number) '_' num2str(numero_tir_fin_old) '_' num2str(numero_tir_fin) '.mat']) |
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[781] | 281 | OutputFile=fullfile_uvmat(RootPath,OutputDir,'signal','.nc','_00001',FileIndex); |
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[780] | 282 | error=struct2nc(OutputFile,Data);%save result file |
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| 283 | if isempty(error) |
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| 284 | disp(['output file ' OutputFile ' written']) |
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| 285 | else |
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| 286 | disp(error) |
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| 287 | end |
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[779] | 288 | end |
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[781] | 289 | numero_tir_fin_old=numero_tir_fin+1% first index for next bloc reading |
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| 290 | if (numero_tir_fin_old+pas_fichier-1)>Nmoy |
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[780] | 291 | test_fin_fichier=-1; |
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| 292 | end |
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[779] | 293 | end |
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| 294 | |
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| 295 | |
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