%'RUN_FIX': function for fixing velocity fields: %----------------------------------------------- % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) % %filename: name of the netcdf file (used as input and output) %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) %.vel_type='civ1' or 'civ2'; %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) %flagindex: flag specifying which values of vec_f are removed: % if flagindex(1)=1: vec_f=-2 vectors are removed % if flagindex(2)=1: vec_f=3 vectors are removed % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) %iter=1 for civ1 fields and iter=2 for civ2 fields %thresh_vecC: threshold in the image correlation vec_C %flag_mask: =1 mask used to remove vectors (0 else) %maskname: name of the mask image file for fix %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold %fileref: .nc file name for a reference velocity (='': refrence 0 used) %fieldref: 'civ1','filter1'...feld used in fileref function error=RUN_FIX(filename,field,flagindex,iter,thresh_vecC,flag_mask,maskname,thresh_vel,inf_sup,fileref,fieldref) error=[]; %default vel_type{1}=field.vel_type; %check writing access [errorread,message]=fileattrib(filename); if ischar(message) msgbox_uvmat('ERROR',[filename ':' message]); return end if ~isequal(message.UserWrite,1) msgbox_uvmat('ERROR',['no writting access to ' filename ' (RUN_FIX.m)']); return end Field=read_civxdata(filename,'ima_cor',field.vel_type); if isfield(Field,'Txt') error=Field.Txt; %error in reading return end if ~isfield(Field,'X') || ~isfield(Field,'Y') || ~isfield(Field,'U') || ~isfield(Field,'V') error=['input file ' filename ' does not contain vectors in RUN_FIX.m']; %bad input file return end if ~isfield(Field,'C') Field.C=ones(size(Field.X));%correlation=1 by default end if ~isfield(Field,'F') Field.F=ones(size(Field.X));%warning flag=1 by default end if ~isfield(Field,'FF') Field.FF=zeros(size(Field.X));%fixflag=0 by default end vec_f_unit=abs(Field.F)-10*double(uint16(abs(Field.F)/10)); %unityterm of vec_F in abs value vec_f_sign=sign(Field.F).*vec_f_unit;% gives the unity digit of vec_f with correct sign flag1=(flagindex(1)==1)&(vec_f_sign==-2);%removed vectors vec_f=-2 flag2=(flagindex(2)==1)&(vec_f_sign==3);%removed vectors vec_f=3 if iter==1 flag3=(flagindex(3)==1)&(vec_f_sign==2); % Hart vectors elseif iter==2 flag3=(flagindex(3)==1)&(vec_f_sign==4); % end flag4=(Field.C < thresh_vecC)&(flag1~=1)&(flag2~=1)&(flag3~=1); % =1 for low vec_C vectors not previously removed % criterium on velocity values delta_u=Field.U;%default without ref file delta_v=Field.V; if exist('fileref','var') && ~isempty(fileref) if ~exist(fileref,'file') error='reference file not found in RUN_FIX.m'; display(error); return end FieldRef=read_civxdata(fileref,[],fieldref); if isfield(FieldRef,'FF') index_true=find(FieldRef.FF==0); FieldRef.X=FieldRef.X(index_true); FieldRef.Y=FieldRef.Y(index_true); FieldRef.U=FieldRef.U(index_true); FieldRef.V=FieldRef.V(index_true); end if ~isfield(FieldRef,'X') || ~isfield(FieldRef,'Y') || ~isfield(FieldRef,'U') || ~isfield(FieldRef,'V') error='reference file is not a velocity field in RUN_FIX.m '; %bad input file return end if length(FieldRef.X)<=1 errordlg('reference field with one vector or less in RUN_FIX.m') return end vec_U_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.U,Field.X,Field.Y); %interpolate vectors in the ref field 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 delta_u=Field.U-vec_U_ref;%take the difference with the interpolated ref field delta_v=Field.V-vec_V_ref; end thresh_vel_x=thresh_vel; thresh_vel_y=thresh_vel; if isequal(inf_sup,1) flag5=abs(delta_u)thresh_vel_x | abs(delta_v)>thresh_vel_y) &(flag1~=1)&(flag2~=1)&(flag3~=1)&(flag4~=1); end % flag7 introduce a grey mask, matrix M if isequal (flag_mask,1) M=imread(maskname); nxy=size(M); M=reshape(M,1,nxy(1)*nxy(2)); rangx0=[0.5 nxy(2)-0.5]; rangy0=[0.5 nxy(1)-0.5]; vec_x1=Field.X-Field.U/2;%beginning points vec_x2=Field.X+Field.U/2;%end points of vectors vec_y1=Field.Y-Field.V/2;%beginning points vec_y2=Field.Y+Field.V/2;%end points of vectors indx=1+round((nxy(2)-1)*(vec_x1-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa vec_x indy=1+round((nxy(1)-1)*(vec_y1-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y test_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside indx=indx.*test_in+(1-test_in); %replace indx by 1 out of the mask range indy=indy.*test_in+(1-test_in); %replace indy by 1 out of the mask range ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector Mvalues=M(ICOMB); flag7b=((20 < Mvalues) & (Mvalues < 200))| ~test_in'; indx=1+round((nxy(2)-1)*(vec_x2-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa Field.X indy=1+round((nxy(1)-1)*(vec_y2-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y test_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside indx=indx.*test_in+(1-test_in); %replace indx by 1 out of the mask range indy=indy.*test_in+(1-test_in); %replace indy by 1 out of the mask range ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector Mvalues=M(ICOMB); flag7e=((Mvalues > 20) & (Mvalues < 200))| ~test_in'; flag7=(flag7b|flag7e)'; else flag7=0; end flagmagenta=flag1|flag2|flag3|flag4|flag5|flag7; fixflag_unit=Field.FF-10*floor(Field.FF/10); %unity term of fix_flag %write fix flags in the netcdf file hhh=which('netcdf.open');% look for built-in matlab netcdf library if ~isequal(hhh,'')% case of new builtin Matlab netcdf library nc=netcdf.open(filename,'NC_WRITE'); netcdf.reDef(nc) if iter==1 netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),'fix1',1) elseif iter==2 netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),'fix2',1) end dimid = netcdf.inqDimID(nc,field.nb); try varid = netcdf.inqVarID(nc,field.fixflag);% look for already existing fixflag variable catch varid=netcdf.defVar(nc,field.fixflag,'double',dimid);%create fixflag variable if it does not exist end netcdf.endDef(nc) netcdf.putVar(nc,varid,fixflag_unit+10*flagmagenta); netcdf.close(nc) else %old netcdf library netcdf_toolbox(filename,Field,flagmagenta,iter,field) end function netcdf_toolbox(filename,Field,flagmagenta,iter,field) nc=netcdf(filename,'write'); %open netcdf file for writing result=redef(nc); if isempty(result), msgbox_uvmat('ERROR','##Bad redef operation.'),end if iter==1 nc.fix=1; elseif iter==2 nc.fix2=1; end nc{field.fixflag}=ncfloat(field.nb); fixflag_unit=Field.FF-10*floor(Field.FF/10); %unity term of fix_flag nc{field.fixflag}(:)=fixflag_unit+10*flagmagenta; close(nc);