1 | %'test_patch_tps': test the optimum value for the spline smmoothing function used in civ_series |
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2 | %------------------------------------------------------------------------ |
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3 | % Method: |
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4 | %open a netcdf file with civ results. |
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5 | |
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6 | % function ParamOut=test_patch_tps (Param) |
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7 | % |
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8 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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9 | % |
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10 | %OUTPUT |
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11 | % ParamOut: sets input parameters when the function is selected, not activated(input Param.Action.RUN=0),=[] when the function is running |
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12 | % |
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13 | %INPUT: |
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14 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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15 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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16 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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17 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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18 | % |
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19 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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20 | % see the current structure Param) |
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21 | % .InputTable: cell of input file names, (several lines for multiple input) |
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22 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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23 | % .OutputSubDir: name of the subdirectory for data outputs |
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24 | % .OutputDirExt: directory extension for data outputs |
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25 | % .Action: .ActionName: name of the current activated function |
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26 | % .ActionPath: path of the current activated function |
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27 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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28 | % .RUN =0 for GUI input, =1 for function activation |
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29 | % .RunMode='local','background', 'cluster': type of function use |
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30 | % |
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31 | % .IndexRange: set the file or frame indices on which the action must be performed |
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32 | % .InputFields: sub structure describing the input fields withfields |
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33 | % .FieldName: name(s) of the field |
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34 | % .VelType: velocity type |
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35 | % .FieldName_1: name of the second field in case of two input series |
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36 | % .VelType_1: velocity type of the second field in case of two input series |
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37 | % .Coord_y: name of y coordinate variable |
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38 | % .Coord_x: name of x coordinate variable |
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39 | |
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40 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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41 | |
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42 | %======================================================================= |
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43 | % Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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44 | % http://www.legi.grenoble-inp.fr |
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45 | % Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr |
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46 | % |
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47 | % This file is part of the toolbox UVMAT. |
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48 | % |
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49 | % UVMAT is free software; you can redistribute it and/or modify |
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50 | % it under the terms of the GNU General Public License as published |
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51 | % by the Free Software Foundation; either version 2 of the license, |
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52 | % or (at your option) any later version. |
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53 | % |
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54 | % UVMAT is distributed in the hope that it will be useful, |
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55 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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56 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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57 | % GNU General Public License (see LICENSE.txt) for more details. |
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58 | %======================================================================= |
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59 | |
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60 | function ParamOut=test_patch_tps (Param) |
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61 | |
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62 | %%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% |
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63 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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64 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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65 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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66 | ParamOut.NbSlice='off'; % edit box nbre of slices made active |
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67 | ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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68 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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69 | ParamOut.FieldTransform = 'off';%can use a transform function |
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70 | ParamOut.ProjObject='off';%cannot use projection object(option 'off'/'on', |
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71 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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72 | ParamOut.OutputDirExt='.test_patch';%set the output dir extension |
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73 | ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice |
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74 | |
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75 | %% root input file(s) and type |
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76 | % check the existence of the first file in the series |
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77 | first_j=[];% note that the function will propose to cover the whole range of indices |
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78 | if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end |
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79 | last_j=[]; |
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80 | if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end |
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81 | PairString=''; |
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82 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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83 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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84 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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85 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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86 | if ~exist(FirstFileName,'file') |
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87 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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88 | return |
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89 | else |
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90 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); |
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91 | LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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92 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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93 | if ~exist(FirstFileName,'file') |
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94 | msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) |
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95 | end |
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96 | end |
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97 | |
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98 | %% check the validity of input file types |
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99 | Data=nc2struct(FirstFileName,[]); |
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100 | if isfield(Data,'CivStage') |
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101 | switch Data.CivStage |
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102 | case {1,2} |
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103 | CivStage='civ1'; |
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104 | MaxDiff=1.5; SubDomainSize=250; FieldSmooth=10; %default |
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105 | case 3 |
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106 | CivStage='civ1'; |
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107 | MaxDiff=Data.Patch1_MaxDiff; |
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108 | SubDomainSize=Data.Patch1_SubDomainSize; |
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109 | FieldSmooth=Data.Patch1_FieldSmooth; |
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110 | case {4,5} |
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111 | CivStage='civ2'; |
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112 | MaxDiff=1.5; SubDomainSize=500; FieldSmooth=2; %default |
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113 | case 6 |
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114 | CivStage='civ2'; |
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115 | MaxDiff=Data.Patch2_MaxDiff; |
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116 | SubDomainSize=Data.Patch2_SubDomainSize; |
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117 | FieldSmooth=Data.Patch2_FieldSmooth; |
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118 | end |
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119 | else |
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120 | msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not a civ data']) |
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121 | return |
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122 | end |
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123 | |
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124 | %% numbers of fields |
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125 | incr_j=1;%default |
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126 | if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j) |
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127 | incr_j=Param.IndexRange.incr_j; |
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128 | end |
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129 | if isempty(first_j)||isempty(last_j) |
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130 | nbfield_j=1; |
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131 | else |
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132 | nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices) |
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133 | end |
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134 | first_i=1;last_i=1;incr_i=1;%default |
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135 | if isfield(Param.IndexRange,'MinIndex_i'); first_i=Param.IndexRange.MinIndex_i; end |
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136 | if isfield(Param.IndexRange,'MaxIndex_i'); last_i=Param.IndexRange.MaxIndex_i; end |
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137 | if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i) |
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138 | incr_i=Param.IndexRange.incr_i; |
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139 | end |
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140 | nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices) |
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141 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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142 | |
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143 | %% setting of intput parameters |
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144 | ListParam={'CivStage';'FieldSmooth';'MaxDiff';'SubDomainSize'}; |
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145 | DefaultValue={CivStage;FieldSmooth;MaxDiff;SubDomainSize}; |
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146 | if isfield(Param,'ActionInput') |
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147 | ParamIn=Param.ActionInput; |
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148 | else |
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149 | ParamIn=[]; |
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150 | end |
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151 | [ParamOut.ActionInput,errormsg] = set_param_input(ListParam,DefaultValue,ParamIn); |
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152 | if ~isempty(errormsg) |
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153 | msgbox_uvmat('ERROR',errormsg) |
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154 | end |
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155 | return |
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156 | end |
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157 | %%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% |
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158 | |
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159 | %% read input parameters from an xml file if input is a file name (batch mode) |
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160 | checkrun=1; |
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161 | RUNHandle=[]; |
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162 | WaitbarHandle=[]; |
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163 | if ischar(Param) |
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164 | Param=xml2struct(Param);% read Param as input file (batch case) |
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165 | checkrun=0; |
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166 | else |
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167 | hseries=findobj(allchild(0),'Tag','series'); |
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168 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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169 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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170 | end |
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171 | |
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172 | %% input preparation |
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173 | RootPath=Param.InputTable{:,1}; |
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174 | RootFile=Param.InputTable{:,3}; |
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175 | NomType=Param.InputTable{:,4}; |
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176 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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177 | % if ~isempty(hdisp),delete(hdisp),end; |
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178 | %%%%%%%%%%%% |
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179 | % The cell array filecell is the list of input file names, while |
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180 | % filecell{iview,fileindex}: |
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181 | % iview: line in the table corresponding to a given file series |
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182 | % fileindex: file index within the file series, |
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183 | % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j |
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184 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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185 | %%%%%%%%%%%% |
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186 | |
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187 | %% output file naming |
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188 | FileExtOut='.nc'; % write result as .png images for image inputsFileInfo.FileType='image' |
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189 | NomTypeOut=NomType; |
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190 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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191 | OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); |
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192 | RootFileOut=RootFile; |
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193 | |
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194 | %% file index parameters |
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195 | |
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196 | Param.InputFields.VelType=Param.ActionInput.CivStage; |
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197 | SubDomainSize=Param.ActionInput.SubDomainSize; |
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198 | MaxDiff=Param.ActionInput.MaxDiff; |
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199 | FieldSmooth=(Param.ActionInput.FieldSmooth)*[0.1 0.2 0.5 1 2 5 10];%scan the smoothing param from 1/10 to 10 current value |
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200 | NbSmooth=numel(FieldSmooth); |
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201 | for irho=1:NbSmooth |
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202 | str=num2str(FieldSmooth(irho)); |
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203 | str=regexprep(str,'\.','p'); |
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204 | Ustr{irho}=['U_' str]; |
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205 | Vstr{irho}=['V_' str]; |
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206 | Xstr{irho}=['X_' str]; |
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207 | Ystr{irho}=['Y_' str]; |
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208 | Dimstr{irho}='NbVec'; |
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209 | str_i{irho}=str; |
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210 | end |
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211 | |
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212 | %% Prepare the structure of output netcdf file |
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213 | DataOut.ListGlobalAttribute={'CivStage'}; |
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214 | DataOut.CivStage=Param.InputFields.VelType; |
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215 | DataOut.ListVarName=[{'FieldSmooth','Diff_rms','NbExclude','FF','X','Y'} Ustr Vstr] ; |
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216 | DataOut.VarDimName=[{'FieldSmooth','FieldSmooth','FieldSmooth','NbVec','NbVec','NbVec'} Dimstr Dimstr]; |
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217 | DataOut.VarAttribute{4}.Role='falseflag'; |
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218 | DataOut.FieldSmooth=FieldSmooth; |
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219 | |
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220 | %% MAIN LOOP |
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221 | for index=1:1%numel(filecell) |
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222 | Data=read_field(filecell{1,index},'civdata',Param.InputFields); |
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223 | ind_good=find(Data.FF==0|Data.FF==20);%keep good civ data, and also the ones excluded by the criterium of discrepancy betwween smoothed and raw fields (FF=20) |
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224 | NbGood=numel(ind_good); |
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225 | Xin=Data.X(ind_good); |
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226 | Yin=Data.Y(ind_good); |
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227 | Uin=Data.U(ind_good); |
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228 | Vin=Data.V(ind_good); |
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229 | tic |
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230 | for irho=1:NbSmooth |
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231 | [SubRange,NbCentres,Coord_tps,U_tps,V_tps,~,U_smooth, V_smooth,~,FFres]=... |
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232 | filter_tps([Xin Yin],Uin,Vin,[],SubDomainSize,FieldSmooth(irho),MaxDiff); |
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233 | if irho==1 |
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234 | DataOut.FF=zeros(size(Xin)); |
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235 | DataOut.X=Xin; |
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236 | DataOut.Y=Yin; |
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237 | figure(1) |
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238 | cla |
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239 | scatter(Xin,Yin,1) |
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240 | for irec=1:size(SubRange,3) |
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241 | rectangle('Position',[SubRange(:,1,irec)' SubRange(:,2,irec)'-SubRange(:,1,irec)']) |
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242 | end |
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243 | title('subdomains for thin shell splines (tps)') |
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244 | end |
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245 | ind_good=find(FFres==0); |
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246 | ind_false=find(FFres~=0); |
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247 | U_Diff=Uin(ind_good)-U_smooth(ind_good); |
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248 | V_Diff=Vin(ind_good)-V_smooth(ind_good); |
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249 | DataOut.Diff_rms(irho)=sqrt(mean(U_Diff.*U_Diff+V_Diff.*V_Diff)/2); |
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250 | DataOut.NbExclude(irho)=(NbGood-numel(ind_good))/NbGood; |
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251 | DataOut.(['U_' str_i{irho}])=U_smooth; |
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252 | DataOut.(['V_' str_i{irho}])=V_smooth; |
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253 | DataOut.FF(ind_false)=FieldSmooth(irho); |
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254 | end |
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255 | time=toc |
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256 | OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1_series{1}(index),[],j1_series{1}(index),j2_series{1}(index)) |
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257 | errormsg=struct2nc(OutputFile,DataOut) |
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258 | end |
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259 | figure |
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260 | semilogx(FieldSmooth,DataOut.Diff_rms,'b',FieldSmooth,DataOut.NbExclude,'r',FieldSmooth,0.1*ones(size(FieldSmooth)),'m') |
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261 | grid on |
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262 | title( [filecell{1,1} ':' Param.InputFields.VelType]) |
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263 | legend({'rms vel. diff. ' ;' ratio excluded vectors';'recommended diff'},'Location','northwest') |
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264 | xlabel('smoothing parameter') |
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265 | ylabel('rms (pixels) and exclusion ratio') |
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266 | OutputFig=fullfile(OutputPath,OutputDir,'plot_rms_diff.png') |
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267 | saveas(2,OutputFig) |
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268 | |
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269 | |
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270 | |
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271 | |
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272 | |
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273 | |
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274 | |
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