1 | %'read_civdata': reads new civ data from netcdf files
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2 | %------------------------------------------------------------------
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3 | %
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4 | % function [Field,VelTypeOut]=read_civdata(FileName,FieldNames,VelType)
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5 | %
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6 | % OUTPUT:
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7 | % Field: structure representing the selected field, containing
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8 | % .Txt: (char string) error message if any
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9 | % .ListGlobalAttribute: list of global attributes containing:
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10 | % .NbCoord: number of vector components
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11 | % .NbDim: number of dimensions (=2 or 3)
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12 | % .Dt: time interval for the corresponding image pair
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13 | % .Time: absolute time (average of the initial image pair)
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14 | % .CivStage: =0,
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15 | % =1, civ1 has been performed only
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16 | % =2, fix1 has been performed
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17 | % =3, pacth1 has been performed
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18 | % =4, civ2 has been performed
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19 | % =5, fix2 has been performed
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20 | % =6, pacth2 has been performed
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21 | % .CoordUnit: 'pixel'
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22 | % .ListVarName: {'X' 'Y' 'U' 'V' 'F' 'FF'}
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23 | % .X, .Y, .Z: set of vector coordinates
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24 | % .U,.V,.W: corresponding set of vector components
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25 | % .F: warning flags
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26 | % .FF: error flag, =0 for good vectors
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27 | % .C: scalar associated with velocity (used for vector colors)
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28 | %
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29 | % VelTypeOut: velocity type corresponding to the selected field: ='civ1','interp1','interp2','civ2'....
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30 | %
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31 | % INPUT:
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32 | % FileName: file name (string).
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33 | % FieldNames =cell of field names to get, which can contain the strings:
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34 | % 'ima_cor': image correlation, vec_c or vec2_C
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35 | % 'vort','div','strain': requires velocity derivatives DUDX...
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36 | % 'error': error estimate (vec_E or vec2_E)
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37 | %
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38 | % VelType : character string indicating the types of velocity fields to read ('civ1','civ2'...)
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39 | % if vel_type=[] or'*', a priority choice, given by vel_type_out{1,2}, is done depending
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40 | % if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
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41 | %
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42 | % FUNCTIONS called:
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43 | % 'varcivx_generator':, sets the names of vaiables to read in the netcdf file
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44 | % 'nc2struct': reads a netcdf file
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45 |
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46 | %=======================================================================
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47 | % Copyright 2008-2018, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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48 | % http://www.legi.grenoble-inp.fr
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49 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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50 | %
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51 | % This file is part of the toolbox UVMAT.
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52 | %
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53 | % UVMAT is free software; you can redistribute it and/or modify
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54 | % it under the terms of the GNU General Public License as published
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55 | % by the Free Software Foundation; either version 2 of the license,
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56 | % or (at your option) any later version.
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57 | %
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58 | % UVMAT is distributed in the hope that it will be useful,
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59 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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60 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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61 | % GNU General Public License (see LICENSE.txt) for more details.
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62 | %=======================================================================
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63 |
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64 | function [Field,VelTypeOut,errormsg]=read_civdata(FileName,FieldNames,VelType)
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65 |
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66 | %% default input
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67 | if ~exist('VelType','var')
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68 | VelType='';
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69 | end
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70 | if isequal(VelType,'*')
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71 | VelType='';
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72 | end
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73 | if isempty(VelType)
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74 | VelType='';
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75 | end
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76 | if ~exist('FieldNames','var')
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77 | FieldNames=[]; %default
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78 | end
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79 | Field=[];
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80 | VelTypeOut=VelType;
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81 | errormsg='';
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82 | if ischar(FieldNames), FieldNames={FieldNames}; end;
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83 | ProjModeRequest='';
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84 | for ilist=1:length(FieldNames)
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85 | if ~isempty(FieldNames{ilist})
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86 | switch FieldNames{ilist}
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87 | case {'U','V','norm(U,V)'}
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88 | if ~strcmp(FieldNames{1},'vec(U,V)')% if the scalar is not used as color of vectors
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89 | ProjModeRequest='interp_lin';
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90 | end
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91 | case {'curl(U,V)','div(U,V)','strain(U,V)'}
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92 | ProjModeRequest='interp_tps';
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93 | end
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94 | end
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95 | end
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96 |
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97 | %% reading data
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98 | Data=nc2struct(FileName,'ListGlobalAttribute','CivStage');
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99 | if isfield(Data,'Txt')
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100 | errormsg=['error in read_civdata: ' Data.Txt];
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101 | return
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102 | end
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103 | % set the list of variables to read and their role
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104 | [varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Data.CivStage);
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105 | if isempty(varlist)
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106 | errormsg=['error in read_civdata: unknow velocity type ' VelType];
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107 | return
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108 | else
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109 | [Field,vardetect]=nc2struct(FileName,varlist);%read the variables in the netcdf file
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110 | end
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111 | if isfield(Field,'Txt')
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112 | errormsg=Field.Txt;
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113 | return
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114 | end
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115 | if vardetect(1)==0
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116 | errormsg=[ 'requested field not available in ' FileName '/' VelType ': need to run patch'];
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117 | return
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118 | end
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119 | switch VelTypeOut
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120 | case {'civ1','filter1'}
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121 | if isfield(Field,'Patch1_SubDomain')
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122 | Field.SubDomain=Field.Patch1_SubDomain;
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123 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
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124 | end
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125 | if isfield(Field,'Civ1_Dt')
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126 | Field.Dt=Field.Civ1_Dt;
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127 | end
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128 | if isfield(Field,'Civ1_Time')
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129 | Field.Time=Field.Civ1_Time;
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130 | end
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131 | case {'civ2','filter2'}
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132 | if isfield(Field,'Patch2_SubDomain')
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133 | Field.SubDomain=Field.Patch2_SubDomain;
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134 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
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135 | end
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136 | if isfield(Field,'Civ2_Dt')
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137 | Field.Dt=Field.Civ2_Dt;
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138 | end
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139 | if isfield(Field,'Civ2_Time')
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140 | Field.Time=Field.Civ2_Time;
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141 | end
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142 | end
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143 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt','Time'}];
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144 | ivar_U_tps=[];
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145 | ivar_V_tps=[];
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146 | var_ind=find(vardetect);
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147 | for ivar=1:numel(var_ind)
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148 | Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
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149 | %Field.VarAttribute{ivar}.Mesh=0.025;%typical mesh for histograms O.025 pixel (used in series)
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150 | Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
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151 | if strcmp(role{var_ind(ivar)},'vector_x')
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152 | Field.VarAttribute{ivar}.FieldName=FieldNames;
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153 | ivar_U=ivar;
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154 | end
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155 | if strcmp(role{var_ind(ivar)},'vector_x_tps')
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156 | Field.VarAttribute{ivar}.FieldName=FieldNames;
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157 | ivar_U_tps=ivar;
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158 | end
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159 | if strcmp(role{var_ind(ivar)},'vector_y')
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160 | Field.VarAttribute{ivar}.FieldName=FieldNames;
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161 | ivar_V=ivar;
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162 | end
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163 | if strcmp(role{var_ind(ivar)},'vector_y_tps')
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164 | Field.VarAttribute{ivar}.FieldName=FieldNames;
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165 | ivar_V_tps=ivar;
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166 | end
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167 | end
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168 | if ~isempty(ivar_U_tps)
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169 | Field.VarAttribute{ivar_U}.VarIndex_tps=ivar_U_tps;
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170 | end
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171 | if ~isempty(ivar_V_tps)
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172 | Field.VarAttribute{ivar_V}.VarIndex_tps=ivar_V_tps;
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173 | end
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174 |
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175 | %% update list of global attributes
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176 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}];
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177 | Field.NbCoord=2;
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178 | Field.NbDim=2;
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179 | Field.TimeUnit='s';
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180 | Field.CoordUnit='pixel';
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181 |
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182 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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183 | % [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
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184 | %INPUT:
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185 | % FieldNames =cell of field names to get, which can contain the strings:
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186 | % 'ima_cor': image correlation, vec_c or vec2_C
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187 | % 'vort','div','strain': requires velocity derivatives DUDX...
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188 | % 'error': error estimate (vec_E or vec2_E)
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189 | %
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190 | % vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
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191 | % if vel_type=[] or'*', a priority choice is done, civ2 considered better than civ1 )
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192 |
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193 | function [var,role,vel_type_out,errormsg]=varcivx_generator(ProjModeRequest,vel_type,CivStage)
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194 |
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195 | %% default input values
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196 | if ~exist('vel_type','var'),vel_type='';end;
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197 | if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
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198 | errormsg='';
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199 |
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200 | %% select the priority order for automatic vel_type selection
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201 | if strcmp(vel_type,'civ2') && strcmp(ProjModeRequest,'derivatives')
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202 | vel_type='filter2';
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203 | elseif strcmp(vel_type,'civ1') && strcmp(ProjModeRequest,'derivatives')
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204 | vel_type='filter1';
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205 | end
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206 | if isempty(vel_type)||strcmp(vel_type,'*')
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207 | vel_type='filter2';% case CivStage >=6
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208 | switch CivStage
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209 | case {4,5}% civ2 available but not filter2
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210 | if strcmp(ProjModeRequest,'derivatives')% derivatives needed
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211 | vel_type='filter1';
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212 | else
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213 | vel_type='civ2';
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214 | end
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215 | case 3
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216 | vel_type='filter1';
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217 | case {1,2}% civ1 available but not filter1
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218 | vel_type='civ1';
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219 | end
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220 | end
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221 |
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222 | var={};
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223 | switch vel_type
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224 | case 'civ1'
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225 | var={'X','Y','Z','U','V','W','C','F','FF';...
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226 | 'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'};
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227 | role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
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228 | % units={'pixel','pixel','pixel','pixel','pixel','pixel','','',''};
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229 | case 'filter1'
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230 | var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentre','NbCentre','NbCentre';...
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231 | 'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U_smooth','Civ1_V_smooth','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',...
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232 | 'Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps','Civ1_W_tps','Civ1_SubRange','Civ1_NbCentre','Civ1_NbCentres','Civ1_NbSites'};
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233 | role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
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234 | 'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary','ancillary'};
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235 | % rmq: NbCentres and NbSites obsolete replaced by NbCentre, kept for consistency with previous data
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236 | case 'civ2'
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237 | var={'X','Y','Z','U','V','W','C','F','FF';...
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238 | 'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF'};
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239 | role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
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240 | case 'filter2'
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241 | var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentre','NbCentre','NbCentre';...
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242 | 'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U_smooth','Civ2_V_smooth','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',...
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243 | 'Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps','','Civ2_SubRange','Civ2_NbCentre','Civ2_NbCentres','Civ2_NbSites'};
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244 | role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
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245 | 'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary','ancillary'};
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246 | end
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247 | if ~strcmp(ProjModeRequest,'interp_tps')
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248 | var=var(:,1:9);%suppress tps if not needed
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249 | end
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250 | vel_type_out=vel_type;
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251 |
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252 |
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253 |
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254 |
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255 |
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