| 1 | %'read_civdata': reads new civ data from netcdf files
|
---|
| 2 | %------------------------------------------------------------------
|
---|
| 3 | %
|
---|
| 4 | % function [Field,VelTypeOut]=read_civdata(FileName,FieldNames,VelType)
|
---|
| 5 | %
|
---|
| 6 | % OUTPUT:
|
---|
| 7 | % Field: structure representing the selected field, containing
|
---|
| 8 | % .Txt: (char string) error message if any
|
---|
| 9 | % .ListGlobalAttribute: list of global attributes containing:
|
---|
| 10 | % .NbCoord: number of vector components
|
---|
| 11 | % .NbDim: number of dimensions (=2 or 3)
|
---|
| 12 | % .Dt: time interval for the corresponding image pair
|
---|
| 13 | % .Time: absolute time (average of the initial image pair)
|
---|
| 14 | % .CivStage: =0,
|
---|
| 15 | % =1, civ1 has been performed only
|
---|
| 16 | % =2, fix1 has been performed
|
---|
| 17 | % =3, pacth1 has been performed
|
---|
| 18 | % =4, civ2 has been performed
|
---|
| 19 | % =5, fix2 has been performed
|
---|
| 20 | % =6, pacth2 has been performed
|
---|
| 21 | % .CoordUnit: 'pixel'
|
---|
| 22 | % .ListVarName: {'X' 'Y' 'U' 'V' 'F' 'FF'}
|
---|
| 23 | % .X, .Y, .Z: set of vector coordinates
|
---|
| 24 | % .U,.V,.W: corresponding set of vector components
|
---|
| 25 | % .F: warning flags
|
---|
| 26 | % .FF: error flag, =0 for good vectors
|
---|
| 27 | % .C: scalar associated with velocity (used for vector colors)
|
---|
| 28 | %
|
---|
| 29 | % VelTypeOut: velocity type corresponding to the selected field: ='civ1','interp1','interp2','civ2'....
|
---|
| 30 | %
|
---|
| 31 | % INPUT:
|
---|
| 32 | % FileName: file name (string).
|
---|
| 33 | % FieldNames =cell of field names to get, which can contain the strings:
|
---|
| 34 | % 'ima_cor': image correlation, vec_c or vec2_C
|
---|
| 35 | % 'vort','div','strain': requires velocity derivatives DUDX...
|
---|
| 36 | % 'error': error estimate (vec_E or vec2_E)
|
---|
| 37 | %
|
---|
| 38 | % VelType : character string indicating the types of velocity fields to read ('civ1','civ2'...)
|
---|
| 39 | % if vel_type=[] or'*', a priority choice, given by vel_type_out{1,2}, is done depending
|
---|
| 40 | % if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
|
---|
| 41 |
|
---|
| 42 |
|
---|
| 43 | % FUNCTIONS called:
|
---|
| 44 | % 'varcivx_generator':, sets the names of vaiables to read in the netcdf file
|
---|
| 45 | % 'nc2struct': reads a netcdf file
|
---|
| 46 |
|
---|
| 47 | function [Field,VelTypeOut,errormsg]=read_civdata(FileName,FieldNames,VelType)
|
---|
| 48 |
|
---|
| 49 | %% default input
|
---|
| 50 | if ~exist('VelType','var')
|
---|
| 51 | VelType='';
|
---|
| 52 | end
|
---|
| 53 | if isequal(VelType,'*')
|
---|
| 54 | VelType='';
|
---|
| 55 | end
|
---|
| 56 | if isempty(VelType)
|
---|
| 57 | VelType='';
|
---|
| 58 | end
|
---|
| 59 | if ~exist('FieldNames','var')
|
---|
| 60 | FieldNames=[]; %default
|
---|
| 61 | end
|
---|
| 62 | Field=[];
|
---|
| 63 | VelTypeOut=VelType;
|
---|
| 64 | errormsg='';
|
---|
| 65 | if ~exist(FileName,'file')
|
---|
| 66 | errormsg=['input file ' FileName ' does not exist'];
|
---|
| 67 | return
|
---|
| 68 | end
|
---|
| 69 | if ischar(FieldNames), FieldNames={FieldNames}; end;
|
---|
| 70 | ProjModeRequest='';
|
---|
| 71 | for ilist=1:length(FieldNames)
|
---|
| 72 | if ~isempty(FieldNames{ilist})
|
---|
| 73 | switch FieldNames{ilist}
|
---|
| 74 | case{'U','V','norm(U,V)'}
|
---|
| 75 | ProjModeRequest='interp_lin';
|
---|
| 76 | case {'curl(U,V)','div(U,V)','strain(U,V)'}
|
---|
| 77 | ProjModeRequest='interp_tps';
|
---|
| 78 | end
|
---|
| 79 | end
|
---|
| 80 | end
|
---|
| 81 |
|
---|
| 82 | %% reading data
|
---|
| 83 | Data=nc2struct(FileName,'ListGlobalAttribute','CivStage');
|
---|
| 84 | if isfield(Data,'Txt')
|
---|
| 85 | erromsg=['error in read_civdata: ' Data.Txt];
|
---|
| 86 | return
|
---|
| 87 | end
|
---|
| 88 | [varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Data.CivStage);
|
---|
| 89 | if isempty(varlist)
|
---|
| 90 | erromsg=['error in read_civdata: unknow velocity type ' VelType];
|
---|
| 91 | return
|
---|
| 92 | else
|
---|
| 93 | [Field,vardetect]=nc2struct(FileName,varlist);%read the variables in the netcdf file
|
---|
| 94 | end
|
---|
| 95 | if isfield(Field,'Txt')
|
---|
| 96 | errormsg=Field.Txt;
|
---|
| 97 | return
|
---|
| 98 | end
|
---|
| 99 | if vardetect(1)==0
|
---|
| 100 | errormsg=[ 'requested field not available in ' FileName '/' VelType ': need to run patch'];
|
---|
| 101 | return
|
---|
| 102 | end
|
---|
| 103 | switch VelTypeOut
|
---|
| 104 | case{'civ1','filter1'}
|
---|
| 105 | if isfield(Field,'Patch1_SubDomain')
|
---|
| 106 | Field.SubDomain=Field.Patch1_SubDomain;
|
---|
| 107 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
|
---|
| 108 | end
|
---|
| 109 | if isfield(Field,'Civ1_Dt')
|
---|
| 110 | Field.Dt=Field.Civ1_Dt;
|
---|
| 111 | end
|
---|
| 112 | if isfield(Field,'Civ1_Time')
|
---|
| 113 | Field.Time=Field.Civ1_Time;
|
---|
| 114 | end
|
---|
| 115 | case{'civ2','filter2'}
|
---|
| 116 | if isfield(Field,'Patch2_SubDomain')
|
---|
| 117 | Field.SubDomain=Field.Patch2_SubDomain;
|
---|
| 118 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
|
---|
| 119 | end
|
---|
| 120 | if isfield(Field,'Civ2_Dt')
|
---|
| 121 | Field.Dt=Field.Civ2_Dt;
|
---|
| 122 | end
|
---|
| 123 | if isfield(Field,'Civ2_Time')
|
---|
| 124 | Field.Time=Field.Civ2_Time;
|
---|
| 125 | end
|
---|
| 126 | end
|
---|
| 127 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt','Time'}];
|
---|
| 128 | ivar_U_tps=[];
|
---|
| 129 | ivar_V_tps=[];
|
---|
| 130 | var_ind=find(vardetect);
|
---|
| 131 | for ivar=1:numel(var_ind)
|
---|
| 132 | Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
|
---|
| 133 | if strcmp(role{var_ind(ivar)},'vector_x')
|
---|
| 134 | Field.VarAttribute{ivar}.FieldName=FieldNames;
|
---|
| 135 | Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
|
---|
| 136 | ivar_U=ivar;
|
---|
| 137 | end
|
---|
| 138 | if strcmp(role{var_ind(ivar)},'vector_x_tps')
|
---|
| 139 | Field.VarAttribute{ivar}.FieldName=FieldNames;
|
---|
| 140 | Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
|
---|
| 141 | ivar_U_tps=ivar;
|
---|
| 142 | end
|
---|
| 143 | if strcmp(role{var_ind(ivar)},'vector_y')
|
---|
| 144 | Field.VarAttribute{ivar}.FieldName=FieldNames;
|
---|
| 145 | Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
|
---|
| 146 | ivar_V=ivar;
|
---|
| 147 | end
|
---|
| 148 | if strcmp(role{var_ind(ivar)},'vector_y_tps')
|
---|
| 149 | Field.VarAttribute{ivar}.FieldName=FieldNames;
|
---|
| 150 | Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
|
---|
| 151 | ivar_V_tps=ivar;
|
---|
| 152 | end
|
---|
| 153 | Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
|
---|
| 154 | end
|
---|
| 155 | if ~isempty(ivar_U_tps)
|
---|
| 156 | Field.VarAttribute{ivar_U}.VarIndex_tps=ivar_U_tps;
|
---|
| 157 | end
|
---|
| 158 | if ~isempty(ivar_V_tps)
|
---|
| 159 | Field.VarAttribute{ivar_V}.VarIndex_tps=ivar_V_tps;
|
---|
| 160 | end
|
---|
| 161 |
|
---|
| 162 | %% update list of global attributes
|
---|
| 163 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}];
|
---|
| 164 | Field.NbCoord=2;
|
---|
| 165 | Field.NbDim=2;
|
---|
| 166 | Field.TimeUnit='s';
|
---|
| 167 | Field.CoordUnit='pixel';
|
---|
| 168 |
|
---|
| 169 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
---|
| 170 | % [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
|
---|
| 171 | %INPUT:
|
---|
| 172 | % FieldNames =cell of field names to get, which can contain the strings:
|
---|
| 173 | % 'ima_cor': image correlation, vec_c or vec2_C
|
---|
| 174 | % 'vort','div','strain': requires velocity derivatives DUDX...
|
---|
| 175 | % 'error': error estimate (vec_E or vec2_E)
|
---|
| 176 | %
|
---|
| 177 | % vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
|
---|
| 178 | % if vel_type=[] or'*', a priority choice is done, civ2 considered better than civ1 )
|
---|
| 179 |
|
---|
| 180 | function [var,role,vel_type_out,errormsg]=varcivx_generator(ProjModeRequest,vel_type,CivStage)
|
---|
| 181 |
|
---|
| 182 | %% default input values
|
---|
| 183 | if ~exist('vel_type','var'),vel_type='';end;
|
---|
| 184 | if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
|
---|
| 185 | errormsg='';
|
---|
| 186 |
|
---|
| 187 | %% select the priority order for automatic vel_type selection
|
---|
| 188 | if strcmp(vel_type,'civ2') && strcmp(ProjModeRequest,'derivatives')
|
---|
| 189 | vel_type='filter2';
|
---|
| 190 | elseif strcmp(vel_type,'civ1') && strcmp(ProjModeRequest,'derivatives')
|
---|
| 191 | vel_type='filter1';
|
---|
| 192 | end
|
---|
| 193 | if isempty(vel_type)||strcmp(vel_type,'*')
|
---|
| 194 | switch CivStage
|
---|
| 195 | case {6} %filter2 available
|
---|
| 196 | vel_type='filter2';
|
---|
| 197 | case {4,5}% civ2 available but not filter2
|
---|
| 198 | if strcmp(ProjModeRequest,'derivatives')% derivatives needed
|
---|
| 199 | vel_type='filter1';
|
---|
| 200 | else
|
---|
| 201 | vel_type='civ2';
|
---|
| 202 | end
|
---|
| 203 | case 3
|
---|
| 204 | vel_type='filter1';
|
---|
| 205 | case {1,2}% civ1 available but not filter1
|
---|
| 206 | vel_type='civ1';
|
---|
| 207 | end
|
---|
| 208 | end
|
---|
| 209 |
|
---|
| 210 | var={};
|
---|
| 211 | switch vel_type
|
---|
| 212 | case 'civ1'
|
---|
| 213 | var={'X','Y','Z','U','V','W','C','F','FF';...
|
---|
| 214 | 'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'};
|
---|
| 215 | role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
|
---|
| 216 | % units={'pixel','pixel','pixel','pixel','pixel','pixel','','',''};
|
---|
| 217 | case 'filter1'
|
---|
| 218 | var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentres','NbCentres';...
|
---|
| 219 | 'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U_smooth','Civ1_V_smooth','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',...
|
---|
| 220 | 'Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps','Civ1_W_tps','Civ1_SubRange','Civ1_NbCentres','Civ1_NbSites'};
|
---|
| 221 | role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
|
---|
| 222 | 'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary'};
|
---|
| 223 | % rmq: NbSites obsolete replaced by NbCentres, kept for consistency with previous data
|
---|
| 224 | case 'civ2'
|
---|
| 225 | var={'X','Y','Z','U','V','W','C','F','FF';...
|
---|
| 226 | 'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF'};
|
---|
| 227 | role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
|
---|
| 228 | case 'filter2'
|
---|
| 229 | var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentres','NbCentres';...
|
---|
| 230 | 'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U_smooth','Civ2_V_smooth','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',...
|
---|
| 231 | 'Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps','','Civ2_SubRange','Civ2_NbCentres','Civ2_NbSites'};
|
---|
| 232 | role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
|
---|
| 233 | 'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary'};
|
---|
| 234 | end
|
---|
| 235 | if ~strcmp(ProjModeRequest,'interp_tps')
|
---|
| 236 | var=var(:,1:9);%suppress tps if not needed
|
---|
| 237 | end
|
---|
| 238 | vel_type_out=vel_type;
|
---|
| 239 |
|
---|
| 240 |
|
---|
| 241 |
|
---|
| 242 |
|
---|
| 243 |
|
---|