source: trunk/src/series/beam_forming.m @ 984

Last change on this file since 984 was 984, checked in by sommeria, 4 years ago

introduce .cine in various functions, improve stero PIV

File size: 13.6 KB
Line 
1%=======================================================================
2% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
3%   http://www.legi.grenoble-inp.fr
4%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
5%
6%     This file is part of the toolbox UVMAT.
7%
8%     UVMAT is free software; you can redistribute it and/or modify
9%     it under the terms of the GNU General Public License as published
10%     by the Free Software Foundation; either version 2 of the license,
11%     or (at your option) any later version.
12%
13%     UVMAT is distributed in the hope that it will be useful,
14%     but WITHOUT ANY WARRANTY; without even the implied warranty of
15%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
16%     GNU General Public License (see LICENSE.txt) for more details.
17%=======================================================================
18
19function ParamOut=beam_forming(Param)
20
21%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
22if isstruct(Param) && isequal(Param.Action.RUN,0)
23    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
24    ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
25    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
26    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
27    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
28    ParamOut.FieldTransform = 'off';%can use a transform function
29    %ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
30    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
31    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
32    index=msgbox_uvmat('INPUT_TXT','index of the series to process (1 to 5)');%choose the i index of the dat files
33    ParamOut.OutputDirExt=['.p_formed_' index];%set the output dir extension
34    hseries=findobj(allchild(0),'Tag','series');
35    hhseries=guidata(hseries);
36    set(hhseries.num_last_i,'String',index)
37    set(hhseries.num_first_i,'String',index)
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
39      %check the input files
40    first_j=[];
41    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
42    PairString='';
43    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
44    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
45    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
46        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
47    if ~exist(FirstFileName,'file')
48        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
49    end
50    return
51end
52
53ParamOut=[]; %default output
54%% read input parameters from an xml file if input is a file name (batch mode)
55checkrun=1;
56if ischar(Param)
57    Param=xml2struct(Param);% read Param as input file (batch case)
58    checkrun=0;
59end
60hseries=findobj(allchild(0),'Tag','series');
61RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
62WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
63
64%% define the directory for result file (with path=RootPath{1})
65OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
66if ~isfield(Param,'InputFields')
67    Param.InputFields.FieldName='';
68end
69
70%% root input file type
71RootPath=Param.InputTable{1,1};
72RootFile=Param.InputTable{1,3};
73SubDir=Param.InputTable{1,2};
74NomType=Param.InputTable{1,4};
75FileExt=Param.InputTable{1,5};
76[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
77%%%%%%%%%%%%
78% The cell array filecell is the list of input file names, while
79% filecell{iview,fileindex}:
80%        iview: line in the table corresponding to a given file series
81%        fileindex: file index within  the file series,
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
83% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
84%%%%%%%%%%%%
85% NbSlice=1;%default
86% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
87%     NbSlice=Param.IndexRange.NbSlice;
88% end
89NbView=numel(i1_series);%number of input file series (lines in InputTable)
90NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
91NbField_i=size(i1_series{1},2); %nb of fields for the i index
92NbField=NbField_j*NbField_i; %total number of fields
93
94%% determine the file type on each line from the first input file
95ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'};
96NcTypeOptions={'netcdf','civx','civdata'};
97for iview=1:NbView
98    if ~exist(filecell{iview,1}','file')
99        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
100        return
101    end
102    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
103    FileType{iview}=FileInfo{iview}.FileType;
104    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
105    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
106    if ~isempty(j1_series{iview})
107        frame_index{iview}=j1_series{iview};
108    else
109        frame_index{iview}=i1_series{iview};
110    end
111end
112
113% clear all
114% close all
115% read_data=1;
116affichage=0;
117% soustraction=0;
118
119%%%%%% Prepare output
120load (fullfile(RootPath,SubDir,[RootFile '.mat']))
121Data.ListGlobalAttribute={'CoordUnit'}; %%TODO: add also time, how to get it  ?????
122Data.CoordUnit='pixel';
123Data.ListVarName={'Coord_x','Coord_y','A'};
124Data.VarDimName={'Coord_x','Coord_y',{'Coord_y','Coord_x'}};
125%Data.Coord_x=5*(nbvoie_reception-0.5)/numel(nbvoie_reception); % totql length of e
126Data.Coord_x=1:65;
127%Data.Coord_z=(1:A)/133 ;% to check from input parameter ....
128Data.Coord_y=1:332;
129%%%%%%
130%
131% while test_fin_fichier>0
132%     if read_data==1
133%directory='manip_lgit';%%%%%%%%%%%%%%%%%
134%name='test';%%%%%%%%%%%%%%%%%
135%         number=2;
136number=str2num(Param.OutputDirExt(11:end));%extract the subsequence index (from 1 to 5)
137numero_tir_fin_old=1%%%%%%% =0 ?????
138pas_fichier=20;%  %20;% nbre of successive shots to read (to account for computer memory limit)
139Nmoy=800;  %%%%% value 20  FOR TEST : to shift to VALUE 8000 set by the .mat file
140
141test_fin_fichier=1;% test to stop input file reading
142while test_fin_fichier>0
143    numero_tir_debut=1;
144    numero_tir_fin=numero_tir_fin_old+pas_fichier-1;
145   
146    %  eval(['load ' directory '\' name '.mat'])
147    matrice_finale=zeros(A,length(nbvoie_reception),numero_tir_fin);%A=nbre of times (coord z)=2650, numero_tir_fin=time index
148    time=(b/rsf+[0:A-1]/rsf); %b=250, rsf=10,
149    freq1=0.5;freq2=1.5;
150    [BB AA]=butter(4,[freq1 freq2]/rsf*2);
151
152    for ii=1:length(nbvoie_reception)%=64
153        %eval(['fid=fopen(''E:\ManipLGITLecoeur\' directory '\' name '_' num2str(number) '_' num2str(nbvoie_reception(ii)) '.dat'',''r'');']);
154        filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,number,[],ii); % input file name
155        fid=fopen(filename);
156        toto=zeros(Nsequence*A*numero_tir_fin+31,1);% Nsequence=1
157        toto=fread(fid,numero_tir_fin*A*Nsequence+31,'int16','ieee-le') ;% why shift by 31 ?????
158        toto=double(bitxor(uint16(toto),uint16(2048)));
159        toto(1:31)=[];toto(numero_tir_fin*A*Nsequence)=mean(toto);
160        fclose(fid);
161       
162        tata=reshape(toto-2048,A,numero_tir_fin);
163        matrice_finale(:,ii,:)=reshape(tata,[A,1,numero_tir_fin]);
164        clear toto tata
165    end
166   
167   % matrice_finale(:,:,numero_tir_debut:numero_tir_fin_old)=[];%%%%%%% first field removed (when numero_tir_fin_old=1) ?????
168     matrice_finale(:,:,numero_tir_debut:numero_tir_fin_old-1)=[];%%%%%%%
169  %  numero_tir_fin=numero_tir_fin-1;  ?????
170    matrice_finale=reshape(filtfilt(BB,AA,matrice_finale(:,:)),size(matrice_finale));% low pass filtered input signal,along first (time) index?
171   
172    % if soustraction==1
173    %     eval(['load moyenne_' name '_' num2str(number) '.mat matrice_finale_moy'])
174    %     for kk=1:size(matrice_finale,3)
175    %         matrice_finale(:,:,kk)=matrice_finale(:,:,kk)-matrice_finale_moy;
176    %     end
177    % end
178    %eval(['save matrice_finale_' num2str(numero_tir_fin_old) '_' num2str(numero_tir_fin) '.mat'])
179   
180    %%%%%%%%%%%%%%Imagerie
181    fe=rsf*1e6;% sampling frequency for receptor (in Hz)
182    cc=1475;%speed of sound
183    hanning_window=25;
184    hanning_vect=hanning(2*hanning_window+1);
185    interval=[1:size(matrice_finale,1)];
186    freq=0:fe/length(interval):fe*(1-1/length(interval));
187   
188    pas_reseau_z=0.75e-3;%0.75e-3
189    pas_reseau_r=0;
190    voie_mean=length(nbvoie_reception)/2;%32;
191    reseau_z=[0:length(nbvoie_reception)-1]*pas_reseau_z;
192    reseau_z=reseau_z-reseau_z(voie_mean);
193    reseau_r=[0:length(nbvoie_reception)-1]*pas_reseau_r;
194    reseau_r=reseau_r-reseau_r(voie_mean);
195   
196    debut_r=(time(1)+20)*1e-6*cc/2;
197    fin_r=(time(end)-20)*1e-6*cc/2;
198   
199    image_r=debut_r:.5e-3:fin_r;
200    image_z=-24e-3:.75e-3:24e-3;
201   
202    image_fin=zeros(length(image_r),length(image_z),size(matrice_finale,3));%size=(332,65,pas_fichier)
203    %image_fin_bis=zeros(length(image_r),length(image_z),size(matrice_finale,3));
204    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
205   
206    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
207    for kk=1:size(matrice_finale,3)
208        disp(kk)
209        signal=squeeze(matrice_finale(interval,:,kk));
210        tata_fft=fft(signal,[],1);%FFT of the time signal size=(2650,64)     
211        if kk==1           
212            matrice_freq_mean=mean(abs(fft(signal,[],1)),2);
213            X=[freq1*1e6 freq2*1e6];
214            [I J]=find(freq>=X(1) & freq<=X(2));
215            int_freq=find(matrice_freq_mean(round(1:length(freq)/2))>max(matrice_freq_mean(round(1:length(freq)/2)))/2);
216            bandwidth=freq(int_freq(end)-int_freq(1));
217            %clear matrice_freq_mean
218        end
219       
220        for ii=1:length(image_r)
221            for jj=1:length(image_z)
222               
223                delay=zeros(length(nbvoie_reception),1);
224                delay=1/cc*sqrt((reseau_z-image_z(jj)).^2+(reseau_r-image_r(ii)).^2);
225               
226                [ind centre_z]=min(abs((reseau_z-image_z(jj))));
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]);
228                delay=delay-delay(centre_z);
229               
230                hanning_vecteur=zeros(1,length(nbvoie_reception));
231                if centre_z>hanning_window & centre_z<(length(nbvoie_reception)-hanning_window)
232                    hanning_vecteur(centre_z+[-hanning_window:hanning_window])=hanning_vect;
233                elseif centre_z<=hanning_window
234                    test=hanning_vect((centre_z+[-hanning_window:hanning_window])>=1);
235                    hanning_vecteur(1:length(test))=test;
236                elseif centre_z>=(length(nbvoie_reception)-hanning_window)
237                    test=hanning_vect((centre_z+[-hanning_window:hanning_window])<=length(nbvoie_reception));
238                    hanning_vecteur(length(nbvoie_reception)+[-length(test)+1:0])=test;
239                end
240                hanning_vecteur=hanning_vecteur/norm(hanning_vecteur);
241                clear test;
242               
243                amplitude_weight=ones(size(signal,1),1)*hanning_vecteur;
244                signal_new_rec=zeros(size(signal,1),length(nbvoie_reception));
245               
246                tata=zeros(size(signal,1),size(signal,2));
247                tata(J,:)=tata_fft(J,:).*exp(1i*2*pi*(freq(J)'*delay));
248                signal_new_rec=2*real(ifft(tata,[],1)).*amplitude_weight;
249                index_interval_utile=find(interval_utile>0 & interval_utile<size(signal,1));
250                toto=zeros(length(index_interval_utile),1);
251                toto=mean(signal_new_rec(interval_utile(index_interval_utile),:),2);
252                image_fin(ii,jj,kk)=sqrt(mean(toto.^2));
253                clear signal_bis interval_utile index_interval_utile hanning_vecteur
254            end
255        end
256    end
257   
258    clear signal_new_em signal_new_rec m delay toto toto_bis tata tata_fft
259   
260    if affichage==1
261        for kk=1:size(image_fin,3)
262           
263            figure(1)
264            imagesc(image_r*1e2,image_z*1e2,image_fin(:,:,kk)'/max(max(image_fin(:,:,kk)))');
265            title(['avec beamforming - energie max = ' num2str(max(max(image_fin(:,:,kk))))])
266            colorbar;
267            xlabel('r (cm)');ylabel('z (cm)');
268            drawnow
269            pause(.2);
270        end
271    end
272   
273    clear matrice_finale
274   
275    %%%%%%% TO ADAPT
276    for iii=1:size(image_fin,3)
277        Data.A=image_fin(:,:,iii);% time lapse decreasesas z coordinate increases.
278        FileIndex=numero_tir_fin - pas_fichier+iii;%%%%%%TO CHECK!!!!!
279        %%%%%%%%%%
280        %eval(['save analyse_' name '_' num2str(number) '_' num2str(numero_tir_fin_old) '_' num2str(numero_tir_fin) '.mat'])
281        OutputFile=fullfile_uvmat(RootPath,OutputDir,'signal','.nc','_00001',FileIndex);
282        error=struct2nc(OutputFile,Data);%save result file
283        if isempty(error)
284            disp(['output file ' OutputFile ' written'])
285        else
286            disp(error)
287        end
288    end
289    numero_tir_fin_old=numero_tir_fin+1% first index for next bloc reading
290     if (numero_tir_fin_old+pas_fichier-1)>Nmoy
291    test_fin_fichier=-1;
292    end
293end
294
295
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