%'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,XI,YI) errormsg=''; VelTypeOut=VelType;%default %% 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,vel_type_out_cell]=varcivx_generator(FieldNames,VelType); [Field,vardetect,ichoice]=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]; return end var_ind=find(vardetect); for ivar=1:min(numel(var_ind),numel(Field.VarAttribute)) 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 if ~isempty(ichoice) VelTypeOut=vel_type_out_cell{ichoice}; end %% renaming for standard conventions %Field.NbCoord=Field.nb_coord; %Field.NbDim=2;%Field.nb_dim; %% CivStage % if isfield(Field,'patch2')&& isequal(Field.patch2,1) % Field.CivStage=6; % elseif isfield(Field,'fix2')&& isequal(Field.fix2,1) % Field.CivStage=5; % elseif isfield(Field,'civ2')&& isequal(Field.civ2,1) % Field.CivStage=4; % elseif isfield(Field,'patch')&& isequal(Field.patch,1) % Field.CivStage=3; % elseif isfield(Field,'fix')&& isequal(Field.fix,1) % Field.CivStage=2; % else % Field.CivStage=1; % end Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}]; % %determine the appropriate constant for time and dt for the PIV pair % test_civ1=isequal(VelTypeOut,'civ1')||isequal(VelTypeOut,'interp1')||isequal(VelTypeOut,'filter1'); % test_civ2=isequal(VelTypeOut,'civ2')||isequal(VelTypeOut,'interp2')||isequal(VelTypeOut,'filter2'); % Field.Time=0; %default % Field.TimeUnit='s'; % if test_civ1 % if isfield(Field,'absolut_time_T0') % Field.Time=double(Field.absolut_time_T0); % Field.dt=double(Field.dt); % else % Field.Txt='the input file is not civx'; % Field.CivStage=0; % Field.dt=0; % end % elseif test_civ2 % Field.Time=double(Field.absolut_time_T0_2); % Field.dt=double(Field.dt2); % else % Field.Txt='the input file is not civx'; % Field.CivStage=0; % Field.dt=0; % end % % % % %% update list of global attributes % List=Field.ListGlobalAttribute; % ind_remove=[]; % for ilist=1:length(List) % switch(List{ilist}) % case {'patch2','fix2','civ2','patch','fix','dt2','absolut_time_T0','absolut_time_T0_2','nb_coord','nb_dim','pixcmx','pixcmy'} % ind_remove=[ind_remove ilist]; % Field=rmfield(Field,List{ilist}); % end % end % List(ind_remove)=[]; % Field.ListGlobalAttribute=[{'NbCoord'},{'NbDim'} List {'Time','TimeUnit','CivStage','CoordUnit'}]; Field.NbCoord=2; Field.NbDim=2; Field.TimeUnit='s'; Field.CoordUnit='pixel'; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % TAKEN FROM read_civxdata NOT USED % [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, given by vel_type_out{1,2}, is done depending % if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1) function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type) %% 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 switch vel_type case 'civ1' var={'X','Y','Z','U','V','W','C','F','FF';... 'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'}; role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'}; units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]}; case 'interp1' var={'X','Y','Z','U','V','W','FF';... 'Civ1_X','Civ1_Y','','Civ1_U_Diff','Civ1_V_Diff','','Civ1_FF'}; role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','errorflag'}; units={'pixel','pixel','pixel','pixel','pixel','pixel',[]}; case 'filter1' var={'X_tps','Y_tps','Z_tps','U_tps','V_tps','W_tps','X_SubRange','Y_SubRange','NbSites';... 'Civ1_X_tps','Civ1_Y_tps','','Civ1_U_tps','Civ1_V_tps','','Civ1_X_SubRange','Civ1_Y_SubRange','Civ1_NbSites'}; role={'','','','','','','','',''}; units={'pixel','pixel','pixel','pixel','pixel','pixel','pixel','pixel',''}; otherwise % if VelType=[] if testpatch var={'X_tps','Y_tps','Z_tps','U_tps','V_tps','W_tps','X_SubRange','Y_SubRange','NbSites';... 'Civ2_X_tps','Civ2_Y_tps','','Civ2_U_tps','Civ2_V_tps','','Civ2_X_SubRange','Civ2_Y_SubRange','Civ2_NbSites';... 'Civ1_X_tps','Civ1_Y_tps','','Civ1_U_tps','Civ1_V_tps','','Civ1_X_SubRange','Civ1_Y_SubRange','Civ1_NbSites'}; role={'','','','','','','',''}; units={'pixel','pixel','pixel','pixel','pixel','pixel','pixel','pixel'}; else var={'X','Y','Z','U','V','W','C','F','FF';... 'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF';... 'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'}; role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'}; units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]}; end end if isempty(vel_type) || isequal(vel_type,'*') %undefined velocity type (civ1,civ2...) if testder vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second vel_type_out{2}='filter1'; else vel_type_out{1}='civ2'; %priority to civ2 for vector reading, civ1 as second priority vel_type_out{2}='civ1'; end elseif isequal(vel_type,'filter') vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second vel_type_out{2}='filter1'; if ~testder vel_type_out{3}='civ1';%civ1 as third priority if derivatives are not needed end elseif testder test_civ1=isequal(vel_type,'civ1')||isequal(vel_type,'interp1')||isequal(vel_type,'filter1'); if test_civ1 vel_type_out{1}='filter1'; %switch to filter for reading spatial derivatives else vel_type_out{1}='filter2'; end else vel_type_out{1}=vel_type;%imposed velocity field end vel_type_out=vel_type_out';