1 | %'read_field': read the fields from files in different formats (netcdf files, images, video) |
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2 | %-------------------------------------------------------------------------- |
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3 | % function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) |
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4 | % |
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5 | % OUTPUT: |
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6 | % Field: matlab structure representing the field |
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7 | % ParamOut: structure representing parameters: |
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8 | % .FieldName; field name |
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9 | % .VelType |
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10 | % .CivStage: stage of civx processing (=0, not Civx, =1 (civ1), =2 (fix1).... |
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11 | % .Npx,.Npy: for images, nbre of pixels in x and y |
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12 | % errormsg: error message, ='' by default |
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13 | % |
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14 | %INPUT |
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15 | % FileName: name of the input file |
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16 | % FileType: type of file, as determined by the function get_file_info.m |
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17 | % ParamIn: movie object or Matlab structure of input parameters |
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18 | % .FieldName: name (char string) of the input field (for Civx data) |
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19 | % .VelType: char string giving the type of velocity data ('civ1', 'filter1', 'civ2'...) |
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20 | % .ColorVar: variable used for vector color |
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21 | % .Npx, .Npy: nbre of pixels along x and y (used for .vol input files) |
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22 | % .TimeDimName: name of the dimension considered as 'time', selected index value then set by input 'num' |
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23 | % num: frame number for movies |
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24 | % |
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25 | % see also read_image.m,read_civxdata.m,read_civdata.m, |
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26 | |
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27 | %======================================================================= |
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28 | % Copyright 2008-2020, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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29 | % http://www.legi.grenoble-inp.fr |
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30 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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31 | % |
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32 | % This file is part of the toolbox UVMAT. |
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33 | % |
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34 | % UVMAT is free software; you can redistribute it and/or modify |
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35 | % it under the terms of the GNU General Public License as published |
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36 | % by the Free Software Foundation; either version 2 of the license, |
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37 | % or (at your option) any later version. |
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38 | % |
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39 | % UVMAT is distributed in the hope that it will be useful, |
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40 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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41 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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42 | % GNU General Public License (see LICENSE.txt) for more details. |
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43 | %======================================================================= |
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44 | |
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45 | function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) |
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46 | %% default output and check input |
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47 | Field=[]; |
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48 | if ~exist('num','var') |
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49 | num=1; |
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50 | end |
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51 | if isempty(num) |
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52 | num=1; |
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53 | end |
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54 | if ~exist('ParamIn','var') |
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55 | ParamIn=[]; |
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56 | end |
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57 | ParamOut=ParamIn;%default |
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58 | errormsg=''; |
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59 | if isempty(regexp(FileName,'^http://'))&& ~exist(FileName,'file') |
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60 | errormsg=['input file ' FileName ' does not exist']; |
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61 | return |
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62 | end |
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63 | A=[]; |
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64 | InputField={}; |
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65 | check_colorvar=0; |
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66 | if isstruct(ParamIn) |
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67 | if isfield(ParamIn,'FieldName') |
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68 | if ischar(ParamIn.FieldName) |
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69 | InputField={ParamIn.FieldName}; |
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70 | else |
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71 | InputField= ParamIn.FieldName; |
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72 | end |
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73 | end |
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74 | check_colorvar=zeros(size(InputField)); |
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75 | if isfield(ParamIn,'ColorVar')&&~isempty(ParamIn.ColorVar) |
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76 | InputField=[ParamIn.FieldName {ParamIn.ColorVar}]; |
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77 | check_colorvar(numel(InputField))=1; |
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78 | end |
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79 | end |
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80 | |
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81 | %% distingush different input file types |
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82 | switch FileType |
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83 | case 'civdata'% new format for civ results |
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84 | [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType); |
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85 | if ~isempty(errormsg),errormsg=['read_civdata / ' errormsg];return,end |
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86 | ParamOut.CivStage=Field.CivStage; |
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87 | case 'pivdata_fluidimage' |
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88 | [Field,ParamOut.VelType,errormsg]=read_pivdata_fluidimage(FileName,InputField,ParamIn.VelType); |
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89 | ParamOut.CivStage=Field.CivStage; |
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90 | case 'civx'% old (obsolete) format for civ results |
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91 | ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default |
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92 | [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType); |
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93 | if ~isempty(errormsg),errormsg=['read_civxdata / ' errormsg];return,end |
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94 | ParamOut.CivStage=Field.CivStage; |
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95 | case 'netcdf'% general netcdf file (not recognized as civ) |
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96 | ListVarName={}; |
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97 | Role={}; |
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98 | ProjModeRequest={}; |
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99 | %ListInputField={}; |
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100 | %checkU=0; |
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101 | %checkV=0; |
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102 | % scan the list InputField |
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103 | Operator=cell(1,numel(InputField)); |
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104 | InputVar=cell(1,numel(InputField)); |
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105 | for ilist=1:numel(InputField) |
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106 | % look for input variables to read |
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107 | r=regexp(InputField{ilist},'(?<Operator>(^vec|^norm))\((?<UName>.+),(?<VName>.+)\)$','names'); |
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108 | if isempty(r)% no operator used |
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109 | ListVarName=[ListVarName InputField(ilist)];%append the variable name |
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110 | %InputVar{ilist}=InputField(ilist); |
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111 | %ListInputField=[ListInputField InputField(ilist)]; |
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112 | if check_colorvar(ilist)% case of field used for vector color |
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113 | Role{numel(ListVarName)}='ancillary';% not projected with interpolation |
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114 | ProjModeRequest{numel(ListVarName)}=''; |
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115 | else |
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116 | Role{numel(ListVarName)}='scalar'; |
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117 | ProjModeRequest{numel(ListVarName)}='interp_lin';%scalar field (requires interpolation for plot) |
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118 | end |
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119 | Operator{numel(ListVarName)}=''; |
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120 | else % an operator 'vec' or 'norm' is used |
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121 | ListVarName=[ListVarName {r.UName}]; % append the variable in the list if not previously listed |
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122 | if strcmp(r.Operator,'norm') |
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123 | if check_colorvar(ilist) |
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124 | Role=[Role {'ancillary'}]; |
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125 | else |
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126 | Role=[Role {'scalar'}]; |
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127 | end |
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128 | else |
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129 | Role=[Role {'vector_x'}]; |
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130 | end |
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131 | %ListInputField=[ListInputField InputField(ilist)]; |
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132 | ListVarName=[ListVarName {r.VName}];% append the variable in the list if not previously listed |
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133 | Role=[Role {'vector_y'}]; |
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134 | %ListInputField=[ListInputField InputField(ilist)]; |
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135 | Operator{numel(ListVarName)-1}=r.Operator; |
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136 | Operator{numel(ListVarName)}=''; |
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137 | if ~check_colorvar(ilist) && strcmp(r.Operator,'norm') |
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138 | ProjModeRequest{numel(ListVarName)}='interp_lin';%scalar field (requires interpolation for plot) |
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139 | ProjModeRequest{numel(ListVarName)-1}='interp_lin';%scalar field (requires interpolation for plot) |
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140 | else |
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141 | ProjModeRequest{numel(ListVarName)}=''; |
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142 | ProjModeRequest{numel(ListVarName)-1}=''; |
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143 | end |
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144 | end |
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145 | end |
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146 | if ~isfield(ParamIn,'Coord_z') |
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147 | ParamIn.Coord_z=[]; |
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148 | end |
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149 | NbCoord=~isempty(ParamIn.Coord_x)+~isempty(ParamIn.Coord_y)+~isempty(ParamIn.Coord_z); |
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150 | if isfield(ParamIn,'TimeDimName')% case of reading of a single time index in a multidimensional array |
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151 | [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeDimName',ParamIn.TimeDimName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVarName]); |
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152 | elseif isfield(ParamIn,'TimeVarName')% case of reading of a single time in a multidimensional array |
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153 | [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeVarName',ParamIn.TimeVarName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVarName]); |
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154 | if numel(num)~=1 |
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155 | NbCoord=NbCoord+1;% adds time coordinate, except if a single time has been selected |
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156 | end |
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157 | else |
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158 | [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVarName]); |
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159 | end |
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160 | if ~isempty(errormsg) |
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161 | return |
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162 | end |
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163 | CheckStructured=1; |
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164 | %scan all the variables |
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165 | NbCoord=0; |
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166 | if ~isempty(ParamIn.Coord_x) |
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167 | index_Coord_x=find(strcmp(ParamIn.Coord_x,Field.ListVarName)); |
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168 | Field.VarAttribute{index_Coord_x}.Role='coord_x';% |
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169 | NbCoord=NbCoord+1; |
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170 | end |
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171 | if ~isempty(ParamIn.Coord_y) |
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172 | if ischar(ParamIn.Coord_y) |
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173 | index_Coord_y=find(strcmp(ParamIn.Coord_y,Field.ListVarName)); |
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174 | Field.VarAttribute{index_Coord_y}.Role='coord_y';% |
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175 | NbCoord=NbCoord+1; |
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176 | else |
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177 | for icoord_y=1:numel(ParamIn.Coord_y) |
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178 | index_Coord_y=find(strcmp(ParamIn.Coord_y{icoord_y},Field.ListVarName)); |
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179 | Field.VarAttribute{index_Coord_y}.Role='coord_y';% |
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180 | NbCoord=NbCoord+1; |
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181 | end |
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182 | end |
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183 | end |
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184 | NbDim=1; |
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185 | if ~isempty(ParamIn.Coord_z) |
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186 | index_Coord_z=find(strcmp(ParamIn.Coord_z,Field.ListVarName)); |
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187 | Field.VarAttribute{index_Coord_z}.Role='coord_z';% |
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188 | NbCoord=NbCoord+1; |
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189 | NbDim=3; |
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190 | elseif ~isempty(ParamIn.FieldName) |
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191 | NbDim=2; |
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192 | end |
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193 | NormName=''; |
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194 | UName=''; |
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195 | VName=''; |
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196 | if numel(Field.ListVarName)>NbCoord % if there are variables beyond coord (exclude 1 D plots) |
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197 | VarAttribute=cell(1,numel(ListVarName)); |
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198 | for ilist=1:numel(ListVarName) |
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199 | index_var=find(strcmp(ListVarName{ilist},Field.ListVarName),1); |
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200 | VarDimName{ilist}=Field.VarDimName{index_var}; |
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201 | DimOrder=[]; |
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202 | if NbDim ==2 |
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203 | DimOrder=[find(strcmp(ParamIn.Coord_y,VarDimName{ilist})) find(strcmp(ParamIn.Coord_x,VarDimName{ilist}))]; |
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204 | elseif NbDim ==3 |
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205 | DimOrder=[find(strcmp(ParamIn.Coord_z,VarDimName{ilist}))... |
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206 | find(strcmp(ParamIn.Coord_y,VarDimName{ilist}))... |
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207 | find(strcmp(ParamIn.Coord_x,VarDimName{ilist}))]; |
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208 | end |
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209 | if ~isempty(DimOrder) |
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210 | Field.(ListVarName{ilist})=permute(Field.(ListVarName{ilist}),DimOrder); |
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211 | VarDimName{ilist}=VarDimName{ilist}(DimOrder); |
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212 | end |
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213 | if numel(Field.VarAttribute)>=index_var |
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214 | VarAttribute{ilist}=Field.VarAttribute{index_var};% read var attributes from input if exist |
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215 | end |
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216 | end |
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217 | check_remove=false(1,numel(Field.ListVarName)); |
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218 | for ilist=1:numel(ListVarName) |
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219 | VarAttribute{ilist}.Role=Role{ilist}; |
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220 | VarAttribute{ilist}.ProjModeRequest=ProjModeRequest{ilist}; |
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221 | if isfield(ParamIn,'FieldName') |
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222 | VarAttribute{ilist}.Operator=Operator{ilist}; |
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223 | end |
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224 | if strcmp(Operator{ilist},'norm') |
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225 | UName=ListVarName{ilist}; |
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226 | VName=ListVarName{ilist+1}; |
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227 | ListVarName{ilist}='norm'; |
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228 | Field.norm=Field.(UName).*Field.(UName)+Field.(VName).*Field.(VName); |
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229 | Field.norm=sqrt(Field.norm); |
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230 | check_remove(ilist+1)=true; |
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231 | VarAttribute{ilist}.Operator=''; |
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232 | end |
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233 | end |
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234 | ListVarName(check_remove)=[]; |
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235 | VarDimName(check_remove)=[]; |
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236 | VarAttribute(check_remove)=[]; |
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237 | Field.ListVarName=[Field.ListVarName(1:NbCoord) ListVarName];% complement the list of vqriables, which may be listed twice |
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238 | Field.VarDimName=[Field.VarDimName(1:NbCoord) VarDimName]; |
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239 | Field.VarAttribute=[Field.VarAttribute(1:NbCoord) VarAttribute]; |
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240 | end |
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241 | |
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242 | case 'video' |
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243 | if strcmp(class(ParamIn),'VideoReader') |
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244 | A=read(ParamIn,num); |
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245 | else |
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246 | ParamOut=VideoReader(FileName); |
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247 | A=read(ParamOut,num); |
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248 | end |
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249 | case 'mmreader' |
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250 | if strcmp(class(ParamIn),'mmreader') |
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251 | A=read(ParamIn,num); |
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252 | else |
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253 | ParamOut=mmreader(FileName); |
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254 | A=read(ParamOut,num); |
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255 | end |
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256 | case 'vol' |
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257 | A=imread(FileName); |
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258 | Npz=size(A,1)/ParamIn.Npy; |
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259 | A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz); |
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260 | A=permute(A,[3 2 1]); |
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261 | case 'multimage' |
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262 | % warning 'off' |
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263 | A=imread(FileName,num); |
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264 | case 'image' |
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265 | A=imread(FileName); |
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266 | case 'rdvision' |
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267 | [A,FileInfo,timestamps,errormsg]=read_rdvision(FileName,num); |
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268 | case 'image_DaVis' |
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269 | Input=readimx(FileName); |
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270 | if numel(Input.Frames)==1 |
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271 | num=1; |
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272 | end |
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273 | A=Input.Frames{num}.Components{1}.Planes{1}'; |
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274 | for ilist=1:numel(Input.Frames{1}.Attributes) |
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275 | if strcmp(Input.Frames{1}.Attributes{ilist}.Name,'AcqTimeSeries') |
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276 | timestamps=str2num(Input.Frames{1}.Attributes{ilist}.Value(1:end-3))/1000000; |
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277 | break |
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278 | end |
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279 | end |
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280 | case 'cine_phantom' |
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281 | [A,FileInfo] = read_cine_phantom(FileName,num ); |
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282 | otherwise |
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283 | errormsg=[ FileType ': invalid input file type for uvmat']; |
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284 | |
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285 | end |
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286 | |
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287 | %% case of image |
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288 | if ~isempty(A) |
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289 | if strcmp(FileType,'rdvision')||strcmp(FileType,'image_DaVis') |
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290 | Field.Time=timestamps; |
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291 | end |
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292 | if isstruct(ParamOut) |
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293 | ParamOut.FieldName='image'; |
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294 | end |
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295 | Npz=1;%default |
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296 | npxy=size(A); |
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297 | Field.NbDim=2;%default |
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298 | Field.AName='image'; |
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299 | Field.ListVarName={'Coord_y','Coord_x','A'}; % |
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300 | Field.VarAttribute{1}.Unit='pixel'; |
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301 | Field.VarAttribute{2}.Unit='pixel'; |
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302 | Field.VarAttribute{1}.Role='coord_y'; |
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303 | Field.VarAttribute{2}.Role='coord_x'; |
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304 | Field.VarAttribute{3}.Role='scalar'; |
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305 | if ndims(A)==3 |
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306 | if Npz==1;%color |
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307 | Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x','rgb'}}; % |
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308 | Field.Coord_y=[npxy(1)-0.5 0.5]; |
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309 | Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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310 | if isstruct(ParamOut) |
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311 | ParamOut.Npx=npxy(2);% display image size on the interface |
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312 | ParamOut.Npy=npxy(1); |
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313 | end |
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314 | else |
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315 | Field.NbDim=3; |
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316 | Field.ListVarName=['AZ' Field.ListVarName]; |
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317 | Field.VarDimName={'AZ','Coord_y','Coord_x',{'AZ','Coord_y','Coord_x'}}; |
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318 | Field.AZ=[npxy(1)-0.5 0.5]; |
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319 | Field.Coord_y=[npxy(2)-0.5 0.5]; |
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320 | Field.Coord_x=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers |
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321 | if isstruct(ParamOut) |
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322 | ParamOut.Npx=npxy(3);% display image size on the interface |
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323 | ParamOut.Npy=npxy(2); |
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324 | end |
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325 | end |
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326 | else |
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327 | Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x'}}; % |
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328 | Field.Coord_y=[npxy(1)-0.5 0.5]; |
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329 | Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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330 | end |
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331 | Field.A=A; |
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332 | Field.CoordUnit='pixel'; %used for mouse_motion |
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333 | end |
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334 | |
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335 | |
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336 | |
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