Changeset 781 for trunk/src/series

Timestamp:

May 29, 2014, 6:17:00 PM (11 years ago)

Author:

sommeria

Message:

 

Location:

trunk/src/series

Files:

• beam_forming.m (modified) (12 diffs)
• civ_input.m (modified) (2 diffs)
• civ_series.m (modified) (6 diffs)

trunk/src/series/beam_forming.m

@@ -4 +4 @@
 if isstruct(Param) && isequal(Param.Action.RUN,0)
     ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
-    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
+    ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
     ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
     ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
@@ -12 +12 @@
     ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
     ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
-    ParamOut.OutputDirExt='.p_formed_1';%set the output dir extension
+    index=msgbox_uvmat('INPUT_TXT','index of the series to process (1 to 5)');%choose the i index of the dat files
+    ParamOut.OutputDirExt=['.p_formed_' index];%set the output dir extension
+    hseries=findobj(allchild(0),'Tag','series');
+    hhseries=guidata(hseries);
+    set(hhseries.num_last_i,'String',index)
+    set(hhseries.num_first_i,'String',index)
     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
       %check the input files
@@ -29 +34 @@
 
 ParamOut=[]; %default output
+%% read input parameters from an xml file if input is a file name (batch mode)
+checkrun=1;
+if ischar(Param)
+    Param=xml2struct(Param);% read Param as input file (batch case)
+    checkrun=0;
+end
 hseries=findobj(allchild(0),'Tag','series');
 RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
@@ -84 +95 @@
 % close all
 % read_data=1;
-affichage=1;
+affichage=0;
 % soustraction=0;
-
-% test_fin_fichier=1;
-pas_fichier=1;
-numero_tir_fin_old=1;
 
 %%%%%% Prepare output 
 load (fullfile(RootPath,SubDir,[RootFile '.mat']))
-Data.ListVarName={'Coord_x','Coord_z','Pressure'};
-Data.VarDimName={'Coord_x','Coord_z',{'Coord_z','Coord_x'}};
-Data.Coord_x=5*(nbvoie_reception-0.5)/numel(nbvoie_reception); % totql length of e
-Data.Coord_z=(1:A)/133 ;% to check from input parameter ....
+Data.ListGlobalAttribute={'CoordUnit'}; %%TODO: add also time, how to get it  ?????
+Data.CoordUnit='pixel';
+Data.ListVarName={'AX','AY','A'};
+Data.VarDimName={'AX','AY',{'AY','AX'}};
+%Data.Coord_x=5*(nbvoie_reception-0.5)/numel(nbvoie_reception); % totql length of e
+Data.AX=1:65;
+%Data.Coord_z=(1:A)/133 ;% to check from input parameter ....
+Data.AY=1:332;
 %%%%%%
 %
@@ -104 +115 @@
 %name='test';%%%%%%%%%%%%%%%%%
 %         number=2;
-number=1; %subsequence index (from 1 to 5)
-OutputDirExt=['.p_formed_' num2str(number)]; %TODO: loop on 'number' from 1 to 5
-numero_tir_fin_old=1;
-pas_fichier=20;% nbre of successive shoots to read (to account for computer memory limit)
-Nmoy=20;  %%%%% value 20  FOR TEST : to shift to VALUE 8000 set by the .mat file
+number=str2num(Param.OutputDirExt(11:end));%extract the subsequence index (from 1 to 5) 
+numero_tir_fin_old=1%%%%%%% =0 ?????
+pas_fichier=20;%  %20;% nbre of successive shots to read (to account for computer memory limit)
+Nmoy=800;  %%%%% value 20  FOR TEST : to shift to VALUE 8000 set by the .mat file
 
 test_fin_fichier=1;% test to stop input file reading
 while test_fin_fichier>0
     numero_tir_debut=1;
-    numero_tir_fin=numero_tir_debut+pas_fichier;
+    numero_tir_fin=numero_tir_fin_old+pas_fichier-1;
     
     %  eval(['load ' directory '\' name '.mat'])
@@ -123 +133 @@
     for ii=1:length(nbvoie_reception)%=64
         %eval(['fid=fopen(''E:\ManipLGITLecoeur\' directory '\' name '_' num2str(number) '_' num2str(nbvoie_reception(ii)) '.dat'',''r'');']);
-        filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,number,[],ii);
+        filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,number,[],ii); % input file name
         fid=fopen(filename);
         toto=zeros(Nsequence*A*numero_tir_fin+31,1);% Nsequence=1
-        toto=fread(fid,numero_tir_fin*A*Nsequence+31,'int16','ieee-le') ;
+        toto=fread(fid,numero_tir_fin*A*Nsequence+31,'int16','ieee-le') ;% why shift by 31 ?????
         toto=double(bitxor(uint16(toto),uint16(2048)));
         toto(1:31)=[];toto(numero_tir_fin*A*Nsequence)=mean(toto);
@@ -136 +146 @@
     end
     
-    matrice_finale(:,:,numero_tir_debut:numero_tir_fin_old)=[];
-    numero_tir_fin=numero_tir_fin-1;
-    matrice_finale=reshape(filtfilt(BB,AA,matrice_finale(:,:)),size(matrice_finale));
+   % matrice_finale(:,:,numero_tir_debut:numero_tir_fin_old)=[];%%%%%%% first field removed (when numero_tir_fin_old=1) ?????
+     matrice_finale(:,:,numero_tir_debut:numero_tir_fin_old-1)=[];%%%%%%% 
+  %  numero_tir_fin=numero_tir_fin-1;  ?????
+    matrice_finale=reshape(filtfilt(BB,AA,matrice_finale(:,:)),size(matrice_finale));% low pass filtered input signal,along first (time) index? 
     
     % if soustraction==1
@@ -149 +160 @@
     
     %%%%%%%%%%%%%%Imagerie
-    fe=rsf*1e6;%acquisition frequency
+    fe=rsf*1e6;% sampling frequency for receptor (in Hz)
     cc=1475;%speed of sound
     hanning_window=25;
@@ -176 +187 @@
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     for kk=1:size(matrice_finale,3)
-        kk
-        tir=kk;
-        signal=squeeze(matrice_finale(interval,:,tir));
-        tata_fft=zeros(size(signal,1),size(signal,2));
-        tata_fft=fft(signal,[],1);
-        
-        if kk==1
-            
+        disp(kk)
+        signal=squeeze(matrice_finale(interval,:,kk));
+        tata_fft=fft(signal,[],1);%FFT of the time signal size=(2650,64)     
+        if kk==1           
             matrice_freq_mean=mean(abs(fft(signal,[],1)),2);
             X=[freq1*1e6 freq2*1e6];
@@ -193 +200 @@
         
         for ii=1:length(image_r)
-            [ii kk]
             for jj=1:length(image_z)
                 
@@ -250 +256 @@
     %%%%%%% TO ADAPT
     for iii=1:size(image_fin,3)
-        Data.Pressure=image_fin(:,:,iii);
+        Data.A=image_fin(:,:,iii);% time lapse decreasesas z coordinate increases.
         FileIndex=numero_tir_fin - pas_fichier+iii;%%%%%%TO CHECK!!!!!
         %%%%%%%%%%
         %eval(['save analyse_' name '_' num2str(number) '_' num2str(numero_tir_fin_old) '_' num2str(numero_tir_fin) '.mat'])
-        OutputDir=[Param.OutputSubDir OutputDirExt];% subdirectory for output files
-        OutputFile=fullfile_uvmat(OutputDir,'','signal','.nc','_00001',FileIndex);
+        OutputFile=fullfile_uvmat(RootPath,OutputDir,'signal','.nc','_00001',FileIndex);
         error=struct2nc(OutputFile,Data);%save result file
         if isempty(error)
@@ -263 +268 @@
         end
     end
-    numero_tir_fin_old=numero_tir_fin+1;
-    if (numero_tir_fin_old+pas_fichier)>Nmoy
+    numero_tir_fin_old=numero_tir_fin+1% first index for next bloc reading
+     if (numero_tir_fin_old+pas_fichier-1)>Nmoy 
     test_fin_fichier=-1;
     end

trunk/src/series/civ_input.m

@@ -97 +97 @@
 NomTypeNc='';
 switch FileType
-    case {'image','multimage','video','mmreader'}
+    case {'image','multimage','video','mmreader','netcdf'}
         NomTypeImaA=NomTypeInput;
         iview_image=1;%line # for the input images
@@ -134 +134 @@
         return
     otherwise 
-        msgbox_uvmat('ERROR','civ_series needs images or civ data as input')
+        msgbox_uvmat('ERROR','civ_series needs images, scalar fields in netcdf format, or civ data as input')
         return
 end

trunk/src/series/civ_series.m

@@ -57 +57 @@
     Data.NbSlice='off'; %nbre of slices ('off' by default)
     Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
-    Data.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
+    Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
     Data.FieldTransform = 'off';%can use a transform function
     Data.ProjObject='off';%can use projection object(option 'off'/'on',
@@ -221 +221 @@
         end
         [FileType_A,FileInfo_A,VideoObject_A]=get_file_type(ImageName_A);
+        if strcmp(FileInfo_A.FileType,'netcdf')
+            FieldName_A=Param.InputFields.FieldName;
+            [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
+            par_civ1.ImageA=DataIn.(FieldName_A);
+        else          
         [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1));
+        end
         ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1),[],j2_series_Civ1(1));
         if ~exist(ImageName_B,'file')
@@ -228 +234 @@
         end
         [FileType_B,FileInfo_B,VideoObject_B]=get_file_type(ImageName_B);
-        [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1));
+        if strcmp(FileInfo_B.FileType,'netcdf')
+            FieldName_B=Param.InputFields.FieldName;
+             [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
+             par_civ1.ImageB=DataIn.(FieldName_B);
+        else
+        [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,Param.InputFields,FrameIndex_B_Civ1(1));
+        end
         NbField=numel(i1_series_Civ1);
     elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1
@@ -237 +249 @@
         end
         [FileType_A,FileInfo_A,VideoObject_A]=get_file_type(ImageName_A);
-        [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ2(1));
+        [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileInfo_A.FileType,VideoObject_A,FrameIndex_A_Civ2(1));
         ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(1),[],j2_series_Civ2(1));
         if ~exist(ImageName_B,'file')
@@ -335 +347 @@
         try
             ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
-            [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
+            if strcmp(FileInfo_A.FileType,'netcdf')
+                FieldName_A=Param.InputFields.FieldName;
+                [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
+                par_civ1.ImageA=DataIn.(FieldName_A);
+            else
+                [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
+            end
             ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
-            [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
+            if strcmp(FileInfo_B.FileType,'netcdf')
+                FieldName_B=Param.InputFields.FieldName;
+                [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
+                par_civ1.ImageB=DataIn.(FieldName_B);
+            else
+                [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
+            end
         catch ME
             if ~isempty(ME.message)
@@ -344 +368 @@
             end
         end
-        par_civ1.ImageWidth=FileInfo_A.Width;
-        par_civ1.ImageHeight=FileInfo_A.Height;
+        par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width;
+        par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height;
         list_param=(fieldnames(Param.ActionInput.Civ1))';
         Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param