source: trunk/src/series/beam_forming.m @ 780

Last change on this file since 780 was 780, checked in by sommeria, 10 years ago

beam_forming updated

File size: 12.0 KB
Line 
1function ParamOut=beam_forming(Param)
2
3%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
4if isstruct(Param) && isequal(Param.Action.RUN,0)
5    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
6    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
7    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
8    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
9    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
10    ParamOut.FieldTransform = 'off';%can use a transform function
11    %ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
12    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
13    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
14    ParamOut.OutputDirExt='.p_formed_1';%set the output dir extension
15    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
16      %check the input files
17    first_j=[];
18    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
19    PairString='';
20    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
21    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
22    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
23        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
24    if ~exist(FirstFileName,'file')
25        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
26    end
27    return
28end
29
30ParamOut=[]; %default output
31hseries=findobj(allchild(0),'Tag','series');
32RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
33WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
34
35%% define the directory for result file (with path=RootPath{1})
36OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
37if ~isfield(Param,'InputFields')
38    Param.InputFields.FieldName='';
39end
40
41%% root input file type
42RootPath=Param.InputTable{1,1};
43RootFile=Param.InputTable{1,3};
44SubDir=Param.InputTable{1,2};
45NomType=Param.InputTable{1,4};
46FileExt=Param.InputTable{1,5};
47[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
48%%%%%%%%%%%%
49% The cell array filecell is the list of input file names, while
50% filecell{iview,fileindex}:
51%        iview: line in the table corresponding to a given file series
52%        fileindex: file index within  the file series,
53% 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
54% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
55%%%%%%%%%%%%
56% NbSlice=1;%default
57% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
58%     NbSlice=Param.IndexRange.NbSlice;
59% end
60NbView=numel(i1_series);%number of input file series (lines in InputTable)
61NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
62NbField_i=size(i1_series{1},2); %nb of fields for the i index
63NbField=NbField_j*NbField_i; %total number of fields
64
65%% determine the file type on each line from the first input file
66ImageTypeOptions={'image','multimage','mmreader','video'};
67NcTypeOptions={'netcdf','civx','civdata'};
68for iview=1:NbView
69    if ~exist(filecell{iview,1}','file')
70        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
71        return
72    end
73    [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1});
74    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
75    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
76    if ~isempty(j1_series{iview})
77        frame_index{iview}=j1_series{iview};
78    else
79        frame_index{iview}=i1_series{iview};
80    end
81end
82
83% clear all
84% close all
85% read_data=1;
86affichage=1;
87% soustraction=0;
88
89% test_fin_fichier=1;
90pas_fichier=1;
91numero_tir_fin_old=1;
92
93%%%%%% Prepare output
94load (fullfile(RootPath,SubDir,[RootFile '.mat']))
95Data.ListVarName={'Coord_x','Coord_z','Pressure'};
96Data.VarDimName={'Coord_x','Coord_z',{'Coord_z','Coord_x'}};
97Data.Coord_x=5*(nbvoie_reception-0.5)/numel(nbvoie_reception); % totql length of e
98Data.Coord_z=(1:A)/133 ;% to check from input parameter ....
99%%%%%%
100%
101% while test_fin_fichier>0
102%     if read_data==1
103%directory='manip_lgit';%%%%%%%%%%%%%%%%%
104%name='test';%%%%%%%%%%%%%%%%%
105%         number=2;
106number=1; %subsequence index (from 1 to 5)
107OutputDirExt=['.p_formed_' num2str(number)]; %TODO: loop on 'number' from 1 to 5
108numero_tir_fin_old=1;
109pas_fichier=20;% nbre of successive shoots to read (to account for computer memory limit)
110Nmoy=20;  %%%%% value 20  FOR TEST : to shift to VALUE 8000 set by the .mat file
111
112test_fin_fichier=1;% test to stop input file reading
113while test_fin_fichier>0
114    numero_tir_debut=1;
115    numero_tir_fin=numero_tir_debut+pas_fichier;
116   
117    %  eval(['load ' directory '\' name '.mat'])
118    matrice_finale=zeros(A,length(nbvoie_reception),numero_tir_fin);%A=nbre of times (coord z)=2650, numero_tir_fin=time index
119    time=(b/rsf+[0:A-1]/rsf); %b=250, rsf=10,
120    freq1=0.5;freq2=1.5;
121    [BB AA]=butter(4,[freq1 freq2]/rsf*2);
122
123    for ii=1:length(nbvoie_reception)%=64
124        %eval(['fid=fopen(''E:\ManipLGITLecoeur\' directory '\' name '_' num2str(number) '_' num2str(nbvoie_reception(ii)) '.dat'',''r'');']);
125        filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,number,[],ii);
126        fid=fopen(filename);
127        toto=zeros(Nsequence*A*numero_tir_fin+31,1);% Nsequence=1
128        toto=fread(fid,numero_tir_fin*A*Nsequence+31,'int16','ieee-le') ;
129        toto=double(bitxor(uint16(toto),uint16(2048)));
130        toto(1:31)=[];toto(numero_tir_fin*A*Nsequence)=mean(toto);
131        fclose(fid);
132       
133        tata=reshape(toto-2048,A,numero_tir_fin);
134        matrice_finale(:,ii,:)=reshape(tata,[A,1,numero_tir_fin]);
135        clear toto tata
136    end
137   
138    matrice_finale(:,:,numero_tir_debut:numero_tir_fin_old)=[];
139    numero_tir_fin=numero_tir_fin-1;
140    matrice_finale=reshape(filtfilt(BB,AA,matrice_finale(:,:)),size(matrice_finale));
141   
142    % if soustraction==1
143    %     eval(['load moyenne_' name '_' num2str(number) '.mat matrice_finale_moy'])
144    %     for kk=1:size(matrice_finale,3)
145    %         matrice_finale(:,:,kk)=matrice_finale(:,:,kk)-matrice_finale_moy;
146    %     end
147    % end
148    %eval(['save matrice_finale_' num2str(numero_tir_fin_old) '_' num2str(numero_tir_fin) '.mat'])
149   
150    %%%%%%%%%%%%%%Imagerie
151    fe=rsf*1e6;%acquisition frequency
152    cc=1475;%speed of sound
153    hanning_window=25;
154    hanning_vect=hanning(2*hanning_window+1);
155    interval=[1:size(matrice_finale,1)];
156    freq=0:fe/length(interval):fe*(1-1/length(interval));
157   
158    pas_reseau_z=0.75e-3;%0.75e-3
159    pas_reseau_r=0;
160    voie_mean=length(nbvoie_reception)/2;%32;
161    reseau_z=[0:length(nbvoie_reception)-1]*pas_reseau_z;
162    reseau_z=reseau_z-reseau_z(voie_mean);
163    reseau_r=[0:length(nbvoie_reception)-1]*pas_reseau_r;
164    reseau_r=reseau_r-reseau_r(voie_mean);
165   
166    debut_r=(time(1)+20)*1e-6*cc/2;
167    fin_r=(time(end)-20)*1e-6*cc/2;
168   
169    image_r=debut_r:.5e-3:fin_r;
170    image_z=-24e-3:.75e-3:24e-3;
171   
172    image_fin=zeros(length(image_r),length(image_z),size(matrice_finale,3));%size=(332,65,pas_fichier)
173    %image_fin_bis=zeros(length(image_r),length(image_z),size(matrice_finale,3));
174    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
175   
176    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
177    for kk=1:size(matrice_finale,3)
178        kk
179        tir=kk;
180        signal=squeeze(matrice_finale(interval,:,tir));
181        tata_fft=zeros(size(signal,1),size(signal,2));
182        tata_fft=fft(signal,[],1);
183       
184        if kk==1
185           
186            matrice_freq_mean=mean(abs(fft(signal,[],1)),2);
187            X=[freq1*1e6 freq2*1e6];
188            [I J]=find(freq>=X(1) & freq<=X(2));
189            int_freq=find(matrice_freq_mean(round(1:length(freq)/2))>max(matrice_freq_mean(round(1:length(freq)/2)))/2);
190            bandwidth=freq(int_freq(end)-int_freq(1));
191            %clear matrice_freq_mean
192        end
193       
194        for ii=1:length(image_r)
195            [ii kk]
196            for jj=1:length(image_z)
197               
198                delay=zeros(length(nbvoie_reception),1);
199                delay=1/cc*sqrt((reseau_z-image_z(jj)).^2+(reseau_r-image_r(ii)).^2);
200               
201                [ind centre_z]=min(abs((reseau_z-image_z(jj))));
202                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]);
203                delay=delay-delay(centre_z);
204               
205                hanning_vecteur=zeros(1,length(nbvoie_reception));
206                if centre_z>hanning_window & centre_z<(length(nbvoie_reception)-hanning_window)
207                    hanning_vecteur(centre_z+[-hanning_window:hanning_window])=hanning_vect;
208                elseif centre_z<=hanning_window
209                    test=hanning_vect((centre_z+[-hanning_window:hanning_window])>=1);
210                    hanning_vecteur(1:length(test))=test;
211                elseif centre_z>=(length(nbvoie_reception)-hanning_window)
212                    test=hanning_vect((centre_z+[-hanning_window:hanning_window])<=length(nbvoie_reception));
213                    hanning_vecteur(length(nbvoie_reception)+[-length(test)+1:0])=test;
214                end
215                hanning_vecteur=hanning_vecteur/norm(hanning_vecteur);
216                clear test;
217               
218                amplitude_weight=ones(size(signal,1),1)*hanning_vecteur;
219                signal_new_rec=zeros(size(signal,1),length(nbvoie_reception));
220               
221                tata=zeros(size(signal,1),size(signal,2));
222                tata(J,:)=tata_fft(J,:).*exp(1i*2*pi*(freq(J)'*delay));
223                signal_new_rec=2*real(ifft(tata,[],1)).*amplitude_weight;
224                index_interval_utile=find(interval_utile>0 & interval_utile<size(signal,1));
225                toto=zeros(length(index_interval_utile),1);
226                toto=mean(signal_new_rec(interval_utile(index_interval_utile),:),2);
227                image_fin(ii,jj,kk)=sqrt(mean(toto.^2));
228                clear signal_bis interval_utile index_interval_utile hanning_vecteur
229            end
230        end
231    end
232   
233    clear signal_new_em signal_new_rec m delay toto toto_bis tata tata_fft
234   
235    if affichage==1
236        for kk=1:size(image_fin,3)
237           
238            figure(1)
239            imagesc(image_r*1e2,image_z*1e2,image_fin(:,:,kk)'/max(max(image_fin(:,:,kk)))');
240            title(['avec beamforming - energie max = ' num2str(max(max(image_fin(:,:,kk))))])
241            colorbar;
242            xlabel('r (cm)');ylabel('z (cm)');
243            drawnow
244            pause(.2);
245        end
246    end
247   
248    clear matrice_finale
249   
250    %%%%%%% TO ADAPT
251    for iii=1:size(image_fin,3)
252        Data.Pressure=image_fin(:,:,iii);
253        FileIndex=numero_tir_fin - pas_fichier+iii;%%%%%%TO CHECK!!!!!
254        %%%%%%%%%%
255        %eval(['save analyse_' name '_' num2str(number) '_' num2str(numero_tir_fin_old) '_' num2str(numero_tir_fin) '.mat'])
256        OutputDir=[Param.OutputSubDir OutputDirExt];% subdirectory for output files
257        OutputFile=fullfile_uvmat(OutputDir,'','signal','.nc','_00001',FileIndex);
258        error=struct2nc(OutputFile,Data);%save result file
259        if isempty(error)
260            disp(['output file ' OutputFile ' written'])
261        else
262            disp(error)
263        end
264    end
265    numero_tir_fin_old=numero_tir_fin+1;
266    if (numero_tir_fin_old+pas_fichier)>Nmoy
267    test_fin_fichier=-1;
268    end
269end
270
271
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