1  %'RUN_FIX': function for fixing velocity fields:


2  %


3  % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)


4  %


5  %filename: name of the netcdf file (used as input and output)


6  %field: structure specifying the field to fix (field.vel_type='civ1' or 'civ2')


7  %flagindex: flag specifying which values of vec_f are removed:


8  % if flagindex(1)=1: vec_f=2 vectors are removed


9  % if flagindex(2)=1: vec_f=3 vectors are removed


10  % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)


11  %iter=1 for civ1 fields and iter=2 for civ2 fields


12  %thresh_vecC: threshold in the image correlation vec_C


13  %flag_mask: =1 mask used to remove vectors (0 else)


14  %maskname: name of the mask image file for fix


15  %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists


16  %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold


17  %fileref: .nc file name for a reference velocity (='': refrence 0 used)


18  %fieldref: 'civ1','filter1'...feld used in fileref


19 


20  function error=RUN_FIX(filename,field,flagindex,iter,thresh_vecC,flag_mask,maskname,thresh_vel,inf_sup,fileref,fieldref)


21  error=[]; %default


22  vel_type{1}=field.vel_type;


23  Field=read_civxdata(filename,[],field.vel_type);


24  if isfield(Field,'Txt')


25  error=Field.Txt; %error in reading


26  return


27  end


28 


29  if ~isfield(Field,'X')  ~isfield(Field,'Y')  ~isfield(Field,'U')  ~isfield(Field,'V')


30  error=['input file ' filename ' does not contain vectors in RUN_FIX.m']; %bad input file


31  return


32  end


33  if ~isfield(Field,'C')


34  Field.C=ones(size(Field.X));%correlation=1 by default


35  end


36  if ~isfield(Field,'F')


37  Field.F=ones(size(Field.X));%warning flag=1 by default


38  end


39  if ~isfield(Field,'FF')


40  Field.FF=zeros(size(Field.X));%fixflag=0 by default


41  end


42 


43  vec_f_unit=abs(Field.F)10*double(uint16(abs(Field.F)/10)); %unityterm of vec_F in abs value


44  vec_f_sign=sign(Field.F).*vec_f_unit;% gives the unity digit of vec_f with correct sign


45  flag1=(flagindex(1)==1)&(vec_f_sign==2);%removed vectors vec_f=2


46  flag2=(flagindex(2)==1)&(vec_f_sign==3);%removed vectors vec_f=3


47  if iter==1


48  flag3=(flagindex(3)==1)&(vec_f_sign==2); % Hart vectors


49  elseif iter==2


50  flag3=(flagindex(3)==1)&(vec_f_sign==4); %


51  end


52  flag4=(Field.C < thresh_vecC)&(flag1~=1)&(flag2~=1)&(flag3~=1); % =1 for low vec_C vectors not previously removed


53 


54  % criterium on velocity values


55  delta_u=Field.U;%default without ref file


56  delta_v=Field.V;


57  if exist('fileref','var') && ~isempty(fileref)


58  if ~exist(fileref,'file')


59  error='reference file not found in RUN_FIX.m';


60  display(error);


61  return


62  end


63  FieldRef=read_civxdata(fileref,[],fieldref);


64  if isfield(FieldRef,'FF')


65  index_true=find(FieldRef.FF==0);


66  FieldRef.X=FieldRef.X(index_true);


67  FieldRef.Y=FieldRef.Y(index_true);


68  FieldRef.U=FieldRef.U(index_true);


69  FieldRef.V=FieldRef.V(index_true);


70  end


71  if ~isfield(FieldRef,'X')  ~isfield(FieldRef,'Y')  ~isfield(FieldRef,'U')  ~isfield(FieldRef,'V')


72  error='reference file is not a velocity field in RUN_FIX.m '; %bad input file


73  return


74  end


75  if length(FieldRef.X)<=1


76  errordlg('reference field with one vector or less in RUN_FIX.m')


77  return


78  end


79  vec_U_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.U,Field.X,Field.Y); %interpolate vectors in the ref field


80  vec_V_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.V,Field.X,Field.Y); %interpolate vectors in the ref field to the positions of the main field


81  delta_u=Field.Uvec_U_ref;%take the difference with the interpolated ref field


82  delta_v=Field.Vvec_V_ref;


83  end


84 


85  thresh_vel_x=thresh_vel;


86  thresh_vel_y=thresh_vel;


87  if isequal(inf_sup,1)


88  flag5=abs(delta_u)<thresh_vel_x & abs(delta_v)<thresh_vel_y &(flag1~=1)&(flag2~=1)&(flag3~=1)&(flag4~=1);


89  elseif isequal(inf_sup,2)


90  flag5=(abs(delta_u)>thresh_vel_x  abs(delta_v)>thresh_vel_y) &(flag1~=1)&(flag2~=1)&(flag3~=1)&(flag4~=1);


91  end


92 


93  % flag7 introduce a grey mask, matrix M


94  if isequal (flag_mask,1)


95  M=imread(maskname);


96  nxy=size(M);


97  M=reshape(M,1,nxy(1)*nxy(2));


98  rangx0=[0.5 nxy(2)0.5];


99  rangy0=[0.5 nxy(1)0.5];


100  vec_x1=Field.XField.U/2;%beginning points


101  vec_x2=Field.X+Field.U/2;%end points of vectors


102  vec_y1=Field.YField.V/2;%beginning points


103  vec_y2=Field.Y+Field.V/2;%end points of vectors


104  indx=1+round((nxy(2)1)*(vec_x1rangx0(1))/(rangx0(2)rangx0(1)));% image index x at abcissa vec_x


105  indy=1+round((nxy(1)1)*(vec_y1rangy0(1))/(rangy0(2)rangy0(1)));% image index y at ordinate vec_y


106  test_in=~(indx < 1 indy < 1  indx > nxy(2) indy > nxy(1)); %=0 out of the mask image, 1 inside


107  indx=indx.*test_in+(1test_in); %replace indx by 1 out of the mask range


108  indy=indy.*test_in+(1test_in); %replace indy by 1 out of the mask range


109  ICOMB=((indx1)*nxy(1)+(nxy(1)+1indy));%determine the indices in the image reshaped in a Matlab vector


110  Mvalues=M(ICOMB);


111  flag7b=((20 < Mvalues) & (Mvalues < 200)) ~test_in';


112  indx=1+round((nxy(2)1)*(vec_x2rangx0(1))/(rangx0(2)rangx0(1)));% image index x at abcissa Field.X


113  indy=1+round((nxy(1)1)*(vec_y2rangy0(1))/(rangy0(2)rangy0(1)));% image index y at ordinate vec_y


114  test_in=~(indx < 1 indy < 1  indx > nxy(2) indy > nxy(1)); %=0 out of the mask image, 1 inside


115  indx=indx.*test_in+(1test_in); %replace indx by 1 out of the mask range


116  indy=indy.*test_in+(1test_in); %replace indy by 1 out of the mask range


117  ICOMB=((indx1)*nxy(1)+(nxy(1)+1indy));%determine the indices in the image reshaped in a Matlab vector


118  Mvalues=M(ICOMB);


119  flag7e=((Mvalues > 20) & (Mvalues < 200)) ~test_in';


120  flag7=(flag7bflag7e)';


121  else


122  flag7=0;


123  end


124  flagmagenta=flag1flag2flag3flag4flag5flag7;


125 


126  %write fix flags


127  [errorread,message]=fileattrib(filename);


128 


129  if ~isempty(message) && ~isequal(message.UserWrite,1)


130  msgbox_uvmat('ERROR',['no writting access to ' filename ' (RUN_FIX.m)']);


131  return


132  end


133  nc=netcdf(filename,'write'); %open netcdf file for writing


134  result=redef(nc);


135  if isempty(result), errordlg('##Bad redef operation.'),end


136  if iter==1


137  nc.fix=1;


138  elseif iter==2


139  nc.fix2=1;


140  end


141  %theDim=nc(field.nb) ;% get the number of velocity vectors


142  nc{field.fixflag}=ncfloat(field.nb);


143  fixflag_unit=Field.FF10*floor(Field.FF/10); %unity term of fix_flag


144  nc{field.fixflag}(:)=fixflag_unit+10*flagmagenta;


145  close(nc);

