%'read_civdata': reads new civ data from netcdf files %------------------------------------------------------------------ % % function [Field,VelTypeOut]=read_civxdata(filename,FieldNames,VelType) % % OUTPUT: % Field: structure representing the selected field, containing % .Txt: (char string) error message if any % .ListGlobalAttribute: list of global attributes containing: % .NbCoord: number of vector components % .NbDim: number of dimensions (=2 or 3) % .dt: time interval for the corresponding image pair % .Time: absolute time (average of the initial image pair) % .CivStage: =0, % =1, civ1 has been performed only % =2, fix1 has been performed % =3, pacth1 has been performed % =4, civ2 has been performed % =5, fix2 has been performed % =6, pacth2 has been performed % .CoordUnit: 'pixel' % .ListVarName: {'X' 'Y' 'U' 'V' 'F' 'FF'} % .X, .Y, .Z: set of vector coordinates % .U,.V,.W: corresponding set of vector components % .F: warning flags % .FF: error flag, =0 for good vectors % .C: scalar associated with velocity (used for vector colors) % .DijU; matrix of spatial derivatives (DijU(1,1,:)=DUDX, % DijU(1,2,:)=DUDY, Dij(2,1,:)=DVDX, DijU(2,2,:)=DVDY % % VelTypeOut: velocity type corresponding to the selected field: ='civ1','interp1','interp2','civ2'.... % % INPUT: % filename: file name (string). % FieldNames =cell of field names to get, which can contain the strings: % 'ima_cor': image correlation, vec_c or vec2_C % 'vort','div','strain': requires velocity derivatives DUDX... % 'error': error estimate (vec_E or vec2_E) % % VelType : character string indicating the types of velocity fields to read ('civ1','civ2'...) % if vel_type=[] or'*', a priority choice, given by vel_type_out{1,2}, is done depending % if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1) % FUNCTIONS called: % 'varcivx_generator':, sets the names of vaiables to read in the netcdf file % 'nc2struct': reads a netcdf file function [Field,VelTypeOut,errormsg]=read_civdata(filename,FieldNames,VelType,CivStage) errormsg=''; %% default input if ~exist('VelType','var') VelType=''; end if isequal(VelType,'*') VelType=''; end if isempty(VelType) VelType=''; end if ~exist('FieldNames','var') FieldNames=[]; %default end %% reading data [varlist,role,units,VelTypeOut]=varcivx_generator(FieldNames,VelType,CivStage); [Field,vardetect]=nc2struct(filename,varlist);%read the variables in the netcdf file if isfield(Field,'Txt') errormsg=Field.Txt; return end if vardetect(1)==0 errormsg=[ 'requested field not available in ' filename '/' VelType ': need to run patch']; return end switch VelTypeOut case{'civ1','civ-filter1','filter1'} Field.Dt=Field.Civ1_Dt; case{'civ2','civ-filter2','filter2'} Field.Dt=Field.Civ2_Dt; end Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt'}]; var_ind=find(vardetect); for ivar=1:numel(var_ind) Field.VarAttribute{ivar}.Role=role{var_ind(ivar)}; Field.VarAttribute{ivar}.Unit=units{var_ind(ivar)}; Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel end Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}]; % %% update list of global attributes Field.NbCoord=2; Field.NbDim=2; Field.TimeUnit='s'; Field.CoordUnit='pixel'; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type) %INPUT: % FieldNames =cell of field names to get, which can contain the strings: % 'ima_cor': image correlation, vec_c or vec2_C % 'vort','div','strain': requires velocity derivatives DUDX... % 'error': error estimate (vec_E or vec2_E) % % vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...) % if vel_type=[] or'*', a priority choice is done, civ2 considered better than civ1 ) function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type,CivStage) %% default input values if ~exist('vel_type','var'),vel_type='';end; if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar if ischar(FieldNames), FieldNames={FieldNames}; end; %% select the priority order for automatic vel_type selection testder=0; testpatch=0; for ilist=1:length(FieldNames) if ~isempty(FieldNames{ilist}) switch FieldNames{ilist} case{'u','v'} testpatch=1; case {'vort','div','strain'} testder=1; end end end if isempty(vel_type) switch CivStage case {6} %filter2 available vel_type='civ2'; case {4,5}% civ2 available but not filter2 if testder% derivatives needed vel_type='civ1'; else vel_type='civ2'; end case {1,2,3}% civ1 available but not civ2 vel_type='civ1'; end end if strcmp(vel_type,'civ2') && testder vel_type='filter2'; elseif strcmp(vel_type,'civ1') && testder vel_type='filter1'; end switch vel_type case 'civ1' var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbSites';... 'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',... 'Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps','Civ1_W_tps','Civ1_SubRange','Civ1_NbSites'}; role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',... 'vector_y_tps','vector_z_tps','ancillary','ancillary'}; units={'pixel','pixel','pixel','pixel','pixel','pixel','','','','pixel','pixel','pixel','pixel','pixel',''}; case 'filter1' var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbSites';... 'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U_smooth','Civ1_V_smooth','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',... 'Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps','Civ1_W_tps','Civ1_SubRange','Civ1_NbSites'}; role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',... 'vector_y_tps','vector_z_tps','ancillary','ancillary'}; units={'pixel','pixel','pixel','pixel','pixel','pixel','','','','pixel','pixel','pixel','pixel','pixel',''}; case 'civ2' var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbSites';... 'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',... 'Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps','','Civ2_SubRange','Civ2_NbSites'}; role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',... 'vector_y_tps','vector_z_tps','ancillary','ancillary'}; units={'pixel','pixel','pixel','pixel','pixel','pixel','','','','pixel','pixel','pixel','pixel','pixel',''}; case 'filter2' var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbSites';... 'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U_smooth','Civ2_V_smooth','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',... 'Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps','','Civ2_SubRange','Civ2_NbSites'}; role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',... 'vector_y_tps','vector_z_tps','ancillary','ancillary'}; units={'pixel','pixel','pixel','pixel','pixel','pixel','','','','pixel','pixel','pixel','pixel','pixel',''}; end vel_type_out=vel_type;