%'read_civdata': reads new civ data from netcdf files %------------------------------------------------------------------ % % function [Field,VelTypeOut]=read_civdata(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) % % 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 %======================================================================= % Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr % % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the license, % or (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (see LICENSE.txt) for more details. %======================================================================= function [Field,VelTypeOut,errormsg]=read_civdata(FileName,FieldNames,VelType) %% 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 Field=[]; VelTypeOut=VelType; errormsg=''; if ischar(FieldNames), FieldNames={FieldNames}; end; ProjModeRequest=''; for ilist=1:length(FieldNames) if ~isempty(FieldNames{ilist}) switch FieldNames{ilist} case {'U','V','norm(U,V)'} if ~strcmp(FieldNames{1},'vec(U,V)')% if the scalar is not used as color of vectors ProjModeRequest='interp_lin'; end case {'curl(U,V)','div(U,V)','strain(U,V)'} ProjModeRequest='interp_tps'; end end end %% reading data [Data,tild,tild,errormsg]=nc2struct(FileName,'ListGlobalAttribute','CivStage'); if ~isempty(errormsg) errormsg=['read_civdata: ' errormsg]; return end % set the list of variables to read and their role [varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Data.CivStage); if isempty(varlist) errormsg=['read_civdata: unknow velocity type ' VelType]; return else [Field,vardetect]=nc2struct(FileName,varlist);%read the variables in the netcdf file end 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','filter1'} if isfield(Field,'Patch1_SubDomain') Field.SubDomain=Field.Patch1_SubDomain; Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}]; end if isfield(Field,'Civ1_Dt') Field.Dt=Field.Civ1_Dt; end if isfield(Field,'Civ1_Time') Field.Time=Field.Civ1_Time; end case {'civ2','filter2'} if isfield(Field,'Patch2_SubDomain') Field.SubDomain=Field.Patch2_SubDomain; Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}]; end if isfield(Field,'Civ2_Dt') Field.Dt=Field.Civ2_Dt; end if isfield(Field,'Civ2_Time') Field.Time=Field.Civ2_Time; end end Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt','Time'}]; ivar_U_tps=[]; ivar_V_tps=[]; var_ind=find(vardetect); for ivar=1:numel(var_ind) Field.VarAttribute{ivar}.Role=role{var_ind(ivar)}; %Field.VarAttribute{ivar}.Mesh=0.025;%typical mesh for histograms O.025 pixel (used in series) Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest; if strcmp(role{var_ind(ivar)},'vector_x') Field.VarAttribute{ivar}.FieldName=FieldNames; ivar_U=ivar; end if strcmp(role{var_ind(ivar)},'vector_x_tps') Field.VarAttribute{ivar}.FieldName=FieldNames; ivar_U_tps=ivar; end if strcmp(role{var_ind(ivar)},'vector_y') Field.VarAttribute{ivar}.FieldName=FieldNames; ivar_V=ivar; end if strcmp(role{var_ind(ivar)},'vector_y_tps') Field.VarAttribute{ivar}.FieldName=FieldNames; ivar_V_tps=ivar; end end if ~isempty(ivar_U_tps) Field.VarAttribute{ivar_U}.VarIndex_tps=ivar_U_tps; end if ~isempty(ivar_V_tps) Field.VarAttribute{ivar_V}.VarIndex_tps=ivar_V_tps; end %% update list of global attributes Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}]; 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,vel_type_out,errormsg]=varcivx_generator(ProjModeRequest,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 errormsg=''; %% select the priority order for automatic vel_type selection if strcmp(vel_type,'civ2') && strcmp(ProjModeRequest,'derivatives') vel_type='filter2'; elseif strcmp(vel_type,'civ1') && strcmp(ProjModeRequest,'derivatives') vel_type='filter1'; end if isempty(vel_type)||strcmp(vel_type,'*') vel_type='filter2';% case CivStage >=6 switch CivStage case {4,5}% civ2 available but not filter2 if strcmp(ProjModeRequest,'derivatives')% derivatives needed vel_type='filter1'; else vel_type='civ2'; end case 3 vel_type='filter1'; case {1,2}% civ1 available but not filter1 vel_type='civ1'; end end var={}; 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 'filter1' var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentre','NbCentre','NbCentre';... '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_NbCentre','Civ1_NbCentres','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','ancillary','ancillary'}; % rmq: NbCentres and NbSites obsolete replaced by NbCentre, kept for consistency with previous data case 'civ2' 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'}; role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'}; case 'filter2' var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentre','NbCentre','NbCentre';... '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_NbCentre','Civ2_NbCentres','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','ancillary','ancillary'}; end if ~strcmp(ProjModeRequest,'interp_tps') var=var(:,1:9);%suppress tps if not needed end vel_type_out=vel_type;