1 | %'RUN_FIX': function for fixing velocity fields:
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2 | %-----------------------------------------------
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3 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
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4 | %
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5 | %filename: name of the netcdf file (used as input and output)
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6 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
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7 | %.vel_type='civ1' or 'civ2';
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8 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
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9 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
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10 | %flagindex: flag specifying which values of vec_f are removed:
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11 | % if flagindex(1)=1: vec_f=-2 vectors are removed
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12 | % if flagindex(2)=1: vec_f=3 vectors are removed
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13 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
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14 | %iter=1 for civ1 fields and iter=2 for civ2 fields
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15 | %thresh_vecC: threshold in the image correlation vec_C
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16 | %flag_mask: =1 mask used to remove vectors (0 else)
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17 | %maskname: name of the mask image file for fix
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18 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
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19 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
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20 | %fileref: .nc file name for a reference velocity (='': refrence 0 used)
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21 | %fieldref: 'civ1','filter1'...feld used in fileref
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22 |
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23 | function error=RUN_FIX(filename,field,flagindex,iter,thresh_vecC,flag_mask,maskname,thresh_vel,inf_sup,fileref,fieldref)
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24 | error=[]; %default
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25 | vel_type{1}=field.vel_type;
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26 | %check writing access
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27 | [errorread,message]=fileattrib(filename);
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28 | if ~isempty(message) && ~isequal(message.UserWrite,1)
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29 | msgbox_uvmat('ERROR',['no writting access to ' filename ' (RUN_FIX.m)']);
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30 | return
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31 | end
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32 | Field=read_civxdata(filename,'ima_cor',field.vel_type);
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33 | if isfield(Field,'Txt')
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34 | error=Field.Txt; %error in reading
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35 | return
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36 | end
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37 |
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38 | if ~isfield(Field,'X') || ~isfield(Field,'Y') || ~isfield(Field,'U') || ~isfield(Field,'V')
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39 | error=['input file ' filename ' does not contain vectors in RUN_FIX.m']; %bad input file
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40 | return
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41 | end
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42 | if ~isfield(Field,'C')
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43 | Field.C=ones(size(Field.X));%correlation=1 by default
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44 | end
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45 | if ~isfield(Field,'F')
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46 | Field.F=ones(size(Field.X));%warning flag=1 by default
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47 | end
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48 | if ~isfield(Field,'FF')
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49 | Field.FF=zeros(size(Field.X));%fixflag=0 by default
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50 | end
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51 |
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52 | vec_f_unit=abs(Field.F)-10*double(uint16(abs(Field.F)/10)); %unityterm of vec_F in abs value
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53 | vec_f_sign=sign(Field.F).*vec_f_unit;% gives the unity digit of vec_f with correct sign
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54 | flag1=(flagindex(1)==1)&(vec_f_sign==-2);%removed vectors vec_f=-2
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55 | flag2=(flagindex(2)==1)&(vec_f_sign==3);%removed vectors vec_f=3
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56 | if iter==1
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57 | flag3=(flagindex(3)==1)&(vec_f_sign==2); % Hart vectors
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58 | elseif iter==2
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59 | flag3=(flagindex(3)==1)&(vec_f_sign==4); %
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60 | end
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61 | flag4=(Field.C < thresh_vecC)&(flag1~=1)&(flag2~=1)&(flag3~=1); % =1 for low vec_C vectors not previously removed
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62 |
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63 | % criterium on velocity values
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64 | delta_u=Field.U;%default without ref file
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65 | delta_v=Field.V;
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66 | if exist('fileref','var') && ~isempty(fileref)
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67 | if ~exist(fileref,'file')
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68 | error='reference file not found in RUN_FIX.m';
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69 | display(error);
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70 | return
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71 | end
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72 | FieldRef=read_civxdata(fileref,[],fieldref);
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73 | if isfield(FieldRef,'FF')
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74 | index_true=find(FieldRef.FF==0);
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75 | FieldRef.X=FieldRef.X(index_true);
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76 | FieldRef.Y=FieldRef.Y(index_true);
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77 | FieldRef.U=FieldRef.U(index_true);
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78 | FieldRef.V=FieldRef.V(index_true);
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79 | end
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80 | if ~isfield(FieldRef,'X') || ~isfield(FieldRef,'Y') || ~isfield(FieldRef,'U') || ~isfield(FieldRef,'V')
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81 | error='reference file is not a velocity field in RUN_FIX.m '; %bad input file
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82 | return
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83 | end
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84 | if length(FieldRef.X)<=1
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85 | errordlg('reference field with one vector or less in RUN_FIX.m')
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86 | return
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87 | end
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88 | vec_U_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.U,Field.X,Field.Y); %interpolate vectors in the ref field
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89 | 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
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90 | delta_u=Field.U-vec_U_ref;%take the difference with the interpolated ref field
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91 | delta_v=Field.V-vec_V_ref;
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92 | end
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93 | thresh_vel_x=thresh_vel;
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94 | thresh_vel_y=thresh_vel;
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95 | if isequal(inf_sup,1)
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96 | flag5=abs(delta_u)<thresh_vel_x & abs(delta_v)<thresh_vel_y &(flag1~=1)&(flag2~=1)&(flag3~=1)&(flag4~=1);
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97 | elseif isequal(inf_sup,2)
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98 | flag5=(abs(delta_u)>thresh_vel_x | abs(delta_v)>thresh_vel_y) &(flag1~=1)&(flag2~=1)&(flag3~=1)&(flag4~=1);
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99 | end
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100 |
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101 | % flag7 introduce a grey mask, matrix M
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102 | if isequal (flag_mask,1)
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103 | M=imread(maskname);
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104 | nxy=size(M);
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105 | M=reshape(M,1,nxy(1)*nxy(2));
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106 | rangx0=[0.5 nxy(2)-0.5];
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107 | rangy0=[0.5 nxy(1)-0.5];
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108 | vec_x1=Field.X-Field.U/2;%beginning points
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109 | vec_x2=Field.X+Field.U/2;%end points of vectors
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110 | vec_y1=Field.Y-Field.V/2;%beginning points
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111 | vec_y2=Field.Y+Field.V/2;%end points of vectors
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112 | indx=1+round((nxy(2)-1)*(vec_x1-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa vec_x
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113 | indy=1+round((nxy(1)-1)*(vec_y1-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y
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114 | test_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside
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115 | indx=indx.*test_in+(1-test_in); %replace indx by 1 out of the mask range
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116 | indy=indy.*test_in+(1-test_in); %replace indy by 1 out of the mask range
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117 | ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector
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118 | Mvalues=M(ICOMB);
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119 | flag7b=((20 < Mvalues) & (Mvalues < 200))| ~test_in';
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120 | indx=1+round((nxy(2)-1)*(vec_x2-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa Field.X
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121 | indy=1+round((nxy(1)-1)*(vec_y2-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y
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122 | test_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside
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123 | indx=indx.*test_in+(1-test_in); %replace indx by 1 out of the mask range
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124 | indy=indy.*test_in+(1-test_in); %replace indy by 1 out of the mask range
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125 | ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector
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126 | Mvalues=M(ICOMB);
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127 | flag7e=((Mvalues > 20) & (Mvalues < 200))| ~test_in';
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128 | flag7=(flag7b|flag7e)';
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129 | else
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130 | flag7=0;
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131 | end
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132 | flagmagenta=flag1|flag2|flag3|flag4|flag5|flag7;
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133 | fixflag_unit=Field.FF-10*floor(Field.FF/10); %unity term of fix_flag
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134 |
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135 | %write fix flags in the netcdf file
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136 | hhh=which('netcdf.open');% look for built-in matlab netcdf library
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137 | if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
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138 | nc=netcdf.open(filename,'NC_WRITE');
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139 | netcdf.reDef(nc)
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140 | if iter==1
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141 | netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),'fix1',1)
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142 | elseif iter==2
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143 | netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),'fix2',1)
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144 | end
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145 | dimid = netcdf.inqDimID(nc,field.nb);
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146 | try
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147 | varid = netcdf.inqVarID(nc,field.fixflag);% look for already existing fixflag variable
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148 | catch
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149 | varid=netcdf.defVar(nc,field.fixflag,'double',dimid);%create fixflag variable if it does not exist
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150 | end
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151 | netcdf.endDef(nc)
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152 | netcdf.putVar(nc,varid,fixflag_unit+10*flagmagenta);
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153 | netcdf.close(nc)
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154 | else %old netcdf library
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155 | netcdf_toolbox(filename,Field,flagmagenta,iter,field)
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156 | end
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157 |
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158 | function netcdf_toolbox(filename,Field,flagmagenta,iter,field)
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159 | nc=netcdf(filename,'write'); %open netcdf file for writing
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160 | result=redef(nc);
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161 | if isempty(result), msgbox_uvmat('ERROR','##Bad redef operation.'),end
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162 | if iter==1
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163 | nc.fix=1;
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164 | elseif iter==2
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165 | nc.fix2=1;
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166 | end
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167 | nc{field.fixflag}=ncfloat(field.nb);
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168 | fixflag_unit=Field.FF-10*floor(Field.FF/10); %unity term of fix_flag
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169 | nc{field.fixflag}(:)=fixflag_unit+10*flagmagenta;
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170 | close(nc);
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