%'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 2008-2018, 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_pivdata_fluidimage(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 ~exist(FileName,'file') errormsg=['input file ' FileName ' does not exist']; return end 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=nc2struct(FileName,'ListGlobalAttribute','CivStage'); % if isfield(Data,'Txt') % erromsg=['error in read_civdata: ' Data.Txt]; % return % end % % set the list of variables to read and their role %[varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Datasets.CivStage); % if isempty(varlist) % erromsg=['error in read_civdata: unknow velocity type ' VelType]; % return % else Datasets=hdf5load(FileName);%read the variables in the netcdf file %[varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Datasets.CivStage); role={'coord_x','coord_y','vector_x','vector_y','ancillary','warnflag','errorflag'}; vardetect=ones(size(role)); Field.ListGlobalAttribute= {'Dt','Time','CivStage'}; Field.Dt=1; Field.Time=0; if isfield(Datasets, 'piv1') Field.CivStage=6; else Field.CivStage=3; end VelTypeOut=VelType; switch VelType case {'civ1','filter1'} Data=Datasets.piv0; VelTypeOut='filter1'; case {'civ2','filter2'} Data=Datasets.piv1; VelTypeOut='filter2'; case '' if isfield(Datasets, 'piv1') Data=Datasets.piv1; VelTypeOut='filter2'; else Data=Datasets.piv0; VelTypeOut='filter1'; end end switch VelType case {'civ1','civ2'} Field.X= double(Data.xs); Field.Y= double(Data.ys); Field.U= double(Data.deltaxs); Field.U(isnan(Field.U)) = 0; Field.V= double(Data.deltays); Field.V(isnan(Field.V)) = 0; case {'filter1','filter2',''} Field.X= double(Data.ixvecs_final); Field.Y= double(Data.iyvecs_final); Field.U= double(Data.deltaxs_final); Field.U(isnan(Field.U)) = 0; Field.V= double(Data.deltays_final); Field.V(isnan(Field.V)) = 0; end Field.ListVarName={'X' 'Y' 'U' 'V' 'C' 'F' 'FF'}; Field.VarDimName={'nb_vec' 'nb_vec' 'nb_vec' 'nb_vec' 'nb_vec' 'nb_vec' 'nb_vec'}; Field.C = double(Data.correls_max); Field.F=zeros(size(Field.U)); Field.F(Data.errors.keys + 1)=1; % !!! convention matlab vs python Field.FF=zeros(size(Field.U)); Field.FF(Data.errors.keys + 1)=1; % 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';