%'read_civxdata': reads civx 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 %======================================================================= % Copyright 2008-2016, 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_civxdata(filename,FieldNames,VelType) errormsg=''; Field=[]; VelTypeOut=[]; DataTest=nc2struct(filename,'ListGlobalAttribute','Conventions','CivStage'); if isfield(DataTest,'Txt') errormsg=['nc2struct / ' DataTest.Txt]; return elseif isequal(DataTest.Conventions,'uvmat/civdata')%test for new civ format [Field,VelTypeOut,errormsg]=read_civdata(filename,FieldNames,VelType,DataTest.CivStage); if ~isempty(errormsg),errormsg=['read_civdata / ' errormsg];end return end %% default input if ~exist('VelType','var') VelType=[]; end if isequal(VelType,'*') VelType=[]; end if ~exist('FieldNames','var') FieldNames=[]; %default end %% reading data VelTypeOut=VelType;%default [var,role,units,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);%determine the names of constants and variables to read [Field,vardetect,ichoice]=nc2struct(filename,var);%read the variables in the netcdf file if isfield(Field,'Txt') errormsg=['nc2struct / ' Field.Txt]; return end if vardetect(1)==0 errormsg=[ 'requested field not available in ' filename '/' VelType]; return end var_ind=find(vardetect); for ilist=1:length(FieldNames) testinterp=isempty(regexp(FieldNames{ilist},'(^vec|^C)', 'once'));%test need for gridded data if testinterp, break;end end for ivar=1:length(var_ind) Field.VarAttribute{ivar}.Role=role{var_ind(ivar)}; Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel if strcmp(role{var_ind(ivar)},'vector_x') Field.VarAttribute{ivar}.FieldName=FieldNames; if testinterp Field.VarAttribute{ivar}.ProjModeRequest='interp_lin'; end end end VelTypeOut=VelType; if ~isempty(ichoice) VelTypeOut=vel_type_out_cell{ichoice}; end %% adjust for Djui: if isfield(Field,'DjUi') Field.ListVarName{end-3}='DjUi'; Field.VarDimName{end-3}=[Field.VarDimName{end-3} {'nb_coord'} {'nb_coord'}]; Field.ListVarName(end-2:end)=[]; Field.VarDimName(end-2:end)=[]; Field.VarAttribute(end-2:end)=[]; end %% renaming for standard conventions Field.NbCoord=Field.nb_coord; Field.NbDim=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 %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 errormsg='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 errormsg='the input file is not civx'; Field.CivStage=0; Field.Dt=0; end %% rescale fields to pixel coordinates if isfield(Field,'pixcmx') Field.pixcmx=double(Field.pixcmx); Field.pixcmy=double(Field.pixcmy); Field.U=Field.U*Field.pixcmx; Field.V=Field.V*Field.pixcmy; Field.X=Field.X*Field.pixcmx; Field.Y=Field.Y*Field.pixcmy; end if ~isequal(Field.Dt,0) Field.U=Field.U*Field.Dt;%translate in px displacement Field.V=Field.V*Field.Dt; if isfield(Field,'DjUi') Field.DjUi(:,1,1)=Field.Dt*Field.DjUi(:,1,1); Field.DjUi(:,2,2)=Field.Dt*Field.DjUi(:,2,2); Field.DjUi(:,1,2)=(Field.pixcmy/Field.pixcmx)*Field.Dt*Field.DjUi(:,1,2); Field.DjUi(:,2,1)=(Field.pixcmx/Field.pixcmy)*Field.Dt*Field.DjUi(:,2,1); end 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','dt','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','Dt','TimeUnit','CivStage','CoordUnit'}]; 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: % 'C': image correlation, vec_c or vec2_C % 'curl','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={'C'};end;%default scalar if ischar(FieldNames), FieldNames={FieldNames}; end; %% select the priority order for automatic vel_type selection testder=0; for ilist=1:length(FieldNames) testder=~isempty(regexp(FieldNames{ilist},'(^curl|^div|^strain)', 'once'));%test need for derivatives if testder, break;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'; %% determine names of netcdf variables to read var={'X','Y','Z','U','V','W','C','F','FF'}; role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'}; units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]}; if testder var=[var {'DjUi(:,1,1)','DjUi(:,1,2)','DjUi(:,2,1)','DjUi(:,2,2)'}]; role=[role {'tensor','tensor','tensor','tensor'}]; units=[units {'pixel','pixel','pixel','pixel'}]; end for ilist=1:length(vel_type_out) var=[var;varname1(vel_type_out{ilist},FieldNames)]; end %------------------------------------------------------------------------ %--- determine var names to read function varin=varname1(vel_type,FieldNames) %------------------------------------------------------------------------ testder=0; C1=''; C2=''; for ilist=1:length(FieldNames) if ~isempty(FieldNames{ilist}) switch FieldNames{ilist} case 'C' %image correlation corresponding to a vel vector C1='vec_C'; C2='vec2_C'; case 'error' C1='vec_E'; C2='vec2_E'; otherwise testder=~isempty(regexp(FieldNames{ilist},'(^curl|^div|strain)', 'once'));%test need for derivatives end end end switch vel_type case 'civ1' varin={'vec_X','vec_Y','vec_Z','vec_U','vec_V','vec_W',C1,'vec_F','vec_FixFlag'}; case 'interp1' varin={'vec_patch_X','vec_patch_Y','','vec_patch0_U','vec_patch0_V','','','',''}; case 'filter1' varin={'vec_patch_X','vec_patch_Y','','vec_patch_U','vec_patch_V','','','',''}; case 'civ2' varin={'vec2_X','vec2_Y','vec2_Z','vec2_U','vec2_V','vec2_W',C2,'vec2_F','vec2_FixFlag'}; case 'interp2' varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch0_U','vec2_patch0_V','vec2_patch0_W','','',''}; case 'filter2' varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch_U','vec2_patch_V','vec2_patch0_W','','',''}; end if testder switch vel_type case 'filter1' varin=[varin {'vec_patch_DUDX','vec_patch_DVDX','vec_patch_DUDY','vec_patch_DVDY'}]; case 'filter2' varin=[varin {'vec2_patch_DUDX','vec2_patch_DVDX','vec2_patch_DUDY','vec2_patch_DVDY'}]; end end