1 | %'merge_proj_volume': concatene several fields from series, project on volumes |
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2 | %------------------------------------------------------------------------ |
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3 | % function ParamOut=merge_proj_volume(Param) |
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4 | %------------------------------------------------------------------------ |
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5 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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6 | % |
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7 | %OUTPUT |
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8 | % ParamOut: sets options in the GUI series.fig needed for the function |
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9 | % |
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10 | %INPUT: |
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11 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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12 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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13 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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14 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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15 | % |
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16 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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17 | % see the current structure Param) |
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18 | % .InputTable: cell of input file names, (several lines for multiple input) |
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19 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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20 | % .OutputSubDir: name of the subdirectory for data outputs |
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21 | % .OutputDirExt: directory extension for data outputs |
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22 | % .Action: .ActionName: name of the current activated function |
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23 | % .ActionPath: path of the current activated function |
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24 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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25 | % .RUN =0 for GUI input, =1 for function activation |
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26 | % .RunMode='local','background', 'cluster': type of function use |
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27 | % |
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28 | % .IndexRange: set the file or frame indices on which the action must be performed |
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29 | % .FieldTransform: .TransformName: name of the selected transform function |
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30 | % .TransformPath: path of the selected transform function |
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31 | % .InputFields: sub structure describing the input fields withfields |
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32 | % .FieldName: name(s) of the field |
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33 | % .VelType: velocity type |
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34 | % .FieldName_1: name of the second field in case of two input series |
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35 | % .VelType_1: velocity type of the second field in case of two input series |
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36 | % .Coord_y: name of y coordinate variable |
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37 | % .Coord_x: name of x coordinate variable |
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38 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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39 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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40 | |
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41 | %======================================================================= |
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42 | % Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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43 | % http://www.legi.grenoble-inp.fr |
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44 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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45 | % |
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46 | % This file is part of the toolbox UVMAT. |
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47 | % |
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48 | % UVMAT is free software; you can redistribute it and/or modify |
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49 | % it under the terms of the GNU General Public License as published |
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50 | % by the Free Software Foundation; either version 2 of the license, |
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51 | % or (at your option) any later version. |
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52 | % |
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53 | % UVMAT is distributed in the hope that it will be useful, |
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54 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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55 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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56 | % GNU General Public License (see LICENSE.txt) for more details. |
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57 | %======================================================================= |
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58 | |
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59 | function ParamOut=merge_proj_volume(Param) |
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60 | |
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61 | %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed |
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62 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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63 | ParamOut.AllowInputSort='on';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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64 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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65 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default) |
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66 | ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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67 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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68 | ParamOut.FieldTransform = 'on';%can use a transform function |
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69 | ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) |
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70 | ParamOut.ProjObject='on';%can 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='.volume';%set the output dir extension |
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73 | ParamOut.OutputFileMode='NbInput_i';% '=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 | %check the input files |
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75 | ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
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76 | first_j=[]; |
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77 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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78 | PairString=''; |
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79 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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80 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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81 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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82 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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83 | if ~exist(FirstFileName,'file') |
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84 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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85 | end |
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86 | return |
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87 | end |
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88 | |
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89 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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90 | ParamOut=[]; %default output |
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91 | RUNHandle=[]; |
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92 | WaitbarHandle=[]; |
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93 | |
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94 | %% read input parameters from an xml file if input is a file name (batch mode) |
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95 | checkrun=1; |
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96 | if ischar(Param) |
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97 | Param=xml2struct(Param);% read Param as input file (batch case) |
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98 | checkrun=0; |
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99 | else |
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100 | hseries=findobj(allchild(0),'Tag','series'); |
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101 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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102 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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103 | end |
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104 | if ~(isfield(Param,'ProjObject') && strcmp(Param.ProjObject.Type,'volume')&& strcmp(Param.ProjObject.ProjMode,'interp_lin')) |
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105 | msgbox_uvmat('ERROR','a projection object of type volume with ProjMode interp_lin must be introduced') |
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106 | return |
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107 | end |
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108 | |
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109 | %% root input file type |
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110 | RootPath=Param.InputTable(:,1); |
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111 | RootFile=Param.InputTable(:,3); |
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112 | SubDir=Param.InputTable(:,2); |
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113 | %NomType=Param.InputTable(:,4); |
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114 | FileExt=Param.InputTable(:,5); |
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115 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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116 | %%%%%%%%%%%% |
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117 | % The cell array filecell is the list of input file names, while |
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118 | % filecell{iview,fileindex}: |
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119 | % iview: line in the table corresponding to a given file series |
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120 | % fileindex: file index within the file series, |
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121 | % 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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122 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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123 | %%%%%%%%%%%% |
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124 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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125 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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126 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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127 | NbField=NbField_j*NbField_i; %total number of fields |
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128 | |
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129 | %% define the name for result file (with path=RootPath{1}) |
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130 | OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files |
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131 | |
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132 | if ~isfield(Param,'InputFields') |
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133 | Param.InputFields.FieldName=''; |
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134 | end |
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135 | |
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136 | |
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137 | %% determine the file type on each line from the first input file |
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138 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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139 | NcTypeOptions={'netcdf','civx','civdata'}; |
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140 | for iview=1:NbView |
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141 | if ~exist(filecell{iview,1}','file') |
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142 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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143 | return |
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144 | end |
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145 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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146 | FileType{iview}=FileInfo{iview}.FileType; |
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147 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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148 | if CheckImage{iview} |
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149 | ParamIn{iview}=MovieObject{iview}; |
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150 | else |
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151 | ParamIn{iview}=Param.InputFields; |
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152 | end |
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153 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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154 | if ~isempty(j1_series{iview}) |
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155 | frame_index{iview}=j1_series{iview}; |
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156 | else |
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157 | frame_index{iview}=i1_series{iview}; |
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158 | end |
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159 | end |
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160 | if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject') |
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161 | disp_uvmat('ERROR','projection on a common grid is needed to concatene images: use a Projection Object of type ''plane'' with ProjMode=''interp_lin''',checkrun) |
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162 | return |
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163 | end |
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164 | |
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165 | %% calibration data and timing: read the ImaDoc files |
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166 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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167 | if size(time,1)>1 |
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168 | diff_time=max(max(diff(time))); |
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169 | if diff_time>0 |
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170 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun) |
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171 | end |
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172 | end |
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173 | if ~isempty(errormsg) |
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174 | disp_uvmat('WARNING',errormsg,checkrun) |
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175 | end |
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176 | time=mean(time,1); %averaged time taken for the merged field |
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177 | |
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178 | %% check calibration data |
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179 | for iview=1:NbView |
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180 | if isfield(XmlData{iview}.GeometryCalib,'CheckVolumeScan') %old convention (<2022) |
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181 | CheckVolumeScan{iview}=XmlData{iview}.GeometryCalib.CheckVolumeScan; |
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182 | XmlData{iview}.Slice.SliceCoord=XmlData{iview}.GeometryCalib.SliceCoord; |
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183 | XmlData{iview}.Slice.SliceAngle=XmlData{iview}.GeometryCalib.SliceAngle; |
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184 | elseif isfield(XmlData{1},'Slice')&& isfield(XmlData{iview}.Slice,'CheckVolumeScan') %new convention (>=2022) |
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185 | CheckVolumeScan{iview}=XmlData{iview}.Slice.CheckVolumeScan; |
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186 | else |
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187 | disp('no volume info in calibration data (xml file)') |
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188 | return |
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189 | end |
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190 | if CheckVolumeScan{iview}==0 |
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191 | disp('input field sereis with volume scan (index j) is needed') |
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192 | return |
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193 | end |
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194 | end |
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195 | |
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196 | %% initiate output field |
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197 | DataVol.ListGlobalAttribute={'Conventions','CoordUnit','Time'}; |
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198 | DataVol.Conventions='uvmat'; |
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199 | DataVol.CoordUnit=XmlData{1}.GeometryCalib.CoordUnit; |
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200 | DataVol.Time=0; %TO UPDATE |
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201 | DataVol.ListVarName={'coord_x','coord_y','coord_z','A'}; |
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202 | DataVol.VarDimName={'coord_x','coord_y','coord_z',{'coord_z','coord_y','coord_x'}}; |
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203 | DataVol.VarAttribute{1}.Role='coord_x'; |
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204 | DataVol.VarAttribute{2}.Role='coord_y'; |
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205 | DataVol.VarAttribute{3}.Role='coord_z'; |
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206 | DataVol.VarAttribute{4}.Role='scalar'; |
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207 | DataVol.coord_x=Param.ProjObject.RangeX(1):Param.ProjObject.DX:Param.ProjObject.RangeX(2); |
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208 | DataVol.coord_y=Param.ProjObject.RangeY(1):Param.ProjObject.DY:Param.ProjObject.RangeY(2); |
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209 | DataVol.coord_z=Param.ProjObject.RangeZ(1):Param.ProjObject.DZ:Param.ProjObject.RangeZ(2); |
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210 | DataVol.A=zeros(numel(DataVol.coord_z),numel(DataVol.coord_y),numel(DataVol.coord_x)); |
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211 | %% coordinate transform or other user defined transform |
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212 | % transform_fct='';%default fct handle |
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213 | % if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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214 | % currentdir=pwd; |
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215 | % cd(Param.FieldTransform.TransformPath) |
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216 | % transform_fct=str2func(Param.FieldTransform.TransformName); |
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217 | % cd (currentdir) |
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218 | % if isfield(Param,'TransformInput') |
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219 | % for iview=1:NbView |
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220 | % XmlData{iview}.TransformInput=Param.TransformInput; |
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221 | % end |
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222 | % end |
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223 | % end |
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224 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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225 | % EDIT FROM HERE |
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226 | |
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227 | % %% output file type |
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228 | if isempty(j1_series{1}) |
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229 | disp('error: no index j for z position label') |
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230 | return |
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231 | end |
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232 | NomTypeOut='_1'; |
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233 | |
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234 | RootFileOut=RootFile{1}; |
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235 | for iview=2:NbView |
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236 | if ~strcmp(RootFile{iview},RootFile{1}) |
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237 | RootFileOut='mproj'; |
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238 | break |
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239 | end |
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240 | end |
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241 | |
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242 | |
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243 | %% MAIN LOOP ON FIELDS |
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244 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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245 | % for i_slice=1:NbSlice |
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246 | % index_slice=i_slice:NbSlice:NbField;% select file indices of the slice |
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247 | % NbFiles=0; |
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248 | % nbmissing=0; |
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249 | |
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250 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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251 | tstart=tic; %used to record the computing time |
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252 | CheckOverwrite=1;%default |
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253 | if isfield(Param,'CheckOverwrite') |
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254 | CheckOverwrite=Param.CheckOverwrite; |
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255 | end |
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256 | |
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257 | |
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258 | for index_i=1:NbField_i |
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259 | AMerge=zeros(NbField_j,numel(DataVol.coord_y),numel(DataVol.coord_x)); |
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260 | for index_j=1:NbField_j |
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261 | index_j |
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262 | %% generating the name of the merged field |
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263 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,'.nc',NomTypeOut,index_i); |
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264 | if ~CheckOverwrite && exist(OutputFile,'file') |
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265 | disp(['existing output file ' OutputFile ' already exists, skip to next field']) |
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266 | continue% skip iteration if the mode overwrite is desactivated and the result file already exists |
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267 | end |
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268 | |
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269 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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270 | Data=cell(1,NbView);%initiate the set Data |
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271 | timeread=zeros(1,NbView); |
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272 | for iview=1:NbView |
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273 | %% reading input file(s) |
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274 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index_j},FileType{iview},ParamIn{iview},frame_index{iview}(index_j)); |
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275 | if ~isempty(errormsg) |
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276 | disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun) |
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277 | return |
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278 | end |
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279 | ListVar=Data{iview}.ListVarName; |
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280 | for ilist=1:numel(ListVar) |
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281 | Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations |
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282 | end |
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283 | % get the time defined in the current file if not already defined from the xml file |
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284 | if ~isempty(time) && isfield(Data{iview},'Time') |
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285 | timeread(iview)=Data{iview}.Time; |
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286 | end |
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287 | Data{iview}.ZIndex=index_j; |
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288 | [X,Y]=meshgrid(DataVol.coord_x,DataVol.coord_y);%grid in physical coordinates |
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289 | Data{iview}=proj_plane(Data{iview},XmlData{iview},X,Y); %project on the common x,y plane |
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290 | end |
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291 | % merge the NbView fields only to merge views from several cameras) |
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292 | |
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293 | % [MergeData,errormsg]=merge_field(ProjData); |
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294 | % if ~isempty(errormsg) |
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295 | % disp_uvmat('ERROR',errormsg,checkrun); |
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296 | % return |
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297 | % end |
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298 | AMerge(index_j,:,:)=Data{iview}.A; |
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299 | |
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300 | %%%%%%%%%%%%%%%% END LOOP FOR VOLUME SCAN %%%%%%%%%%%%%%%% |
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301 | end |
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302 | %interpolate on the vertical grid |
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303 | Z=zeros(1,NbField_j); |
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304 | for j_index=1:numel(DataVol.coord_y) |
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305 | for i_index=1:numel(DataVol.coord_x) |
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306 | for ZIndex=1:NbField_j |
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307 | Z(ZIndex)=Zpos(XmlData{iview},ZIndex,X(j_index,i_index),Y(j_index,i_index)); |
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308 | end |
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309 | DataVol.A(:,j_index,i_index) = interp1(Z,AMerge(:,j_index,i_index),DataVol.coord_z); |
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310 | end |
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311 | end |
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312 | error=struct2nc(OutputFile,DataVol)%save result file |
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313 | |
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314 | |
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315 | % if index==1 |
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316 | % TimeData.ListGlobalAttribute={'Conventions','Project','CoordUnit','TimeUnit','ZPos','Time'}; |
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317 | % TimeData.Conventions='uvmat'; |
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318 | % TimeData.Project='2016_Circumpolar'; |
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319 | % TimeData.CoordUnit='cm'; |
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320 | % TimeData.TimeUnit='s'; |
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321 | % % TimeData.ZPos=ZPos; |
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322 | % TimeData.ListVarName={'radius','azimuth','U','V','curl','div'}; |
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323 | % TimeData.VarDimName={'radius','azimuth',{'radius','azimuth'},{'radius','azimuth'}... |
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324 | % {'radius','azimuth'},{'radius','azimuth'}}; |
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325 | % TimeData.VarAttribute{1}.Role=''; |
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326 | % TimeData.VarAttribute{2}.Role=''; |
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327 | % TimeData.VarAttribute{3}.Role='vector_x'; |
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328 | % TimeData.VarAttribute{4}.Role='vector_y'; |
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329 | % TimeData.VarAttribute{5}.Role='scalar'; |
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330 | % TimeData.VarAttribute{6}.Role='scalar'; |
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331 | % |
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332 | % end |
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333 | % |
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334 | % %% append data to the netcdf file for next iterations |
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335 | % |
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336 | % |
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337 | % error=struct2nc(OutputFile,TimeData);%save result file |
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338 | % if isempty(error) |
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339 | % disp(['output file ' OutputFile ' written']) |
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340 | % else |
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341 | % disp(error) |
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342 | % end |
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343 | % ellapsed_time=toc(tstart); |
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344 | % disp(['ellapsed time since start ' num2str(ellapsed_time/60,2) ' minutes']) |
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345 | end |
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346 | |
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347 | % disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration']) |
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348 | |
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349 | % %'merge_field': concatene fields |
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350 | % %------------------------------------------------------------------------ |
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351 | % function [MergeData,errormsg]=merge_field(Data) |
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352 | % %% default output |
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353 | % if isempty(Data)||~iscell(Data) |
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354 | % MergeData=[]; |
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355 | % return |
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356 | % end |
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357 | % errormsg=''; |
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358 | % MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field |
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359 | % NbView=length(Data); |
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360 | % if NbView==1% if there is only one field, just reproduce it in MergeData |
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361 | % return |
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362 | % end |
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363 | % |
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364 | % %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
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365 | % [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); |
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366 | % if ~isempty(errormsg) |
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367 | % return |
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368 | % end |
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369 | % |
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370 | % %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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371 | % for icell=1:length(CellInfo) |
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372 | % if NbDim(icell)~=1 % skip field cells which are of dim 1 |
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373 | % switch CellInfo{icell}.CoordType |
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374 | % case 'scattered' %case of input fields with unstructured coordinates: just concatene data |
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375 | % for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
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376 | % VarName=Data{1}.ListVarName{ivar}; |
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377 | % for iview=2:NbView |
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378 | % MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
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379 | % end |
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380 | % end |
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381 | % case 'grid' %case of fields defined on a structured grid |
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382 | % FFName=''; |
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383 | % if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) |
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384 | % FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable |
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385 | % MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) |
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386 | % MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; |
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387 | % MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; |
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388 | % end |
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389 | % % select good data on each view |
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390 | % for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
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391 | % VarName=Data{1}.ListVarName{ivar}; |
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392 | % for iview=1:NbView |
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393 | % if isempty(FFName) |
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394 | % check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else |
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395 | % else |
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396 | % check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else |
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397 | % end |
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398 | % Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
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399 | % if iview==1 |
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400 | % %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field |
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401 | % MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
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402 | % NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point |
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403 | % elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) |
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404 | % errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; |
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405 | % return |
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406 | % else |
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407 | % MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data |
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408 | % NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else |
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409 | % end |
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410 | % end |
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411 | % MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point |
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412 | % MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data |
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413 | % end |
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414 | % end |
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415 | % |
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416 | % end |
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417 | % end |
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418 | |
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419 | % get the X position corresponding to X,Y for a given plane (labelled by ZIndex) |
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420 | |
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421 | function Z=Zpos(XmlData,ZIndex,X,Y)% Z positions correspoonding to X,Y positions |
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422 | Z=XmlData.Slice.SliceCoord(ZIndex,3)*ones(size(X)); |
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423 | if isfield(XmlData.Slice,'SliceAngle')&&~isequal(XmlData.Slice.SliceAngle,[0 0 0]) |
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424 | [norm_plane(1), norm_plane(2), norm_plane(3)] =rotate_vector(XmlData.SliceAngle(ZIndex,:)*pi/180,0,0,1); |
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425 | Z=Z-(norm_plane(1)*(X-XmlData.Slice.SliceCoord(ZIndex,1))+norm_plane(2)*(Y-XmlData.Slice.SliceCoord(ZIndex,2)))/norm_plane(3); |
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426 | end |
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427 | |
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428 | % proj_plane: poject each image on a common grid given by coord_x and coord_y |
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429 | function DataOut=proj_plane(DataIn,XmlData,X,Y) |
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430 | |
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431 | DataOut=DataIn; %default output |
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432 | |
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433 | %% initial image coordinates |
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434 | [npy,npx]=size(DataIn.A); |
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435 | xima=0.5:npx-0.5;%image coordinates of corners |
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436 | yima=npy-0.5:-1:0.5; |
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437 | [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates |
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438 | |
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439 | %% projected coordinates |
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440 | Z=Zpos(XmlData,DataIn.ZIndex,X,Y);% Z positions correspoonding to X,Y positions |
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441 | |
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442 | %% interpolation on the new grid |
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443 | [XIMA,YIMA]=px_XYZ(XmlData.GeometryCalib,XmlData.Slice,X,Y,Z);% image coordinates for each point in the real |
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444 | DataOut.A=interp2(XIMA_init,YIMA_init,DataIn.A,XIMA,YIMA); |
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445 | |
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446 | |
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447 | |
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448 | |
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449 | |
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450 | %'merge_field': concatene fields |
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451 | %------------------------------------------------------------------------ |
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452 | function [MergeData,errormsg]=merge_field(Data) |
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453 | %% default output |
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454 | if isempty(Data)||~iscell(Data) |
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455 | MergeData=[]; |
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456 | return |
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457 | end |
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458 | errormsg=''; |
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459 | MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field |
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460 | NbView=length(Data); |
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461 | if NbView==1% if there is only one field, just reproduce it in MergeData |
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462 | return |
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463 | end |
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464 | |
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465 | %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
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466 | [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); |
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467 | if ~isempty(errormsg) |
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468 | return |
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469 | end |
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470 | |
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471 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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472 | for icell=1:length(CellInfo) |
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473 | if NbDim(icell)~=1 % skip field cells which are of dim 1 |
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474 | switch CellInfo{icell}.CoordType |
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475 | case 'scattered' %case of input fields with unstructured coordinates: just concatene data |
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476 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
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477 | VarName=Data{1}.ListVarName{ivar}; |
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478 | for iview=2:NbView |
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479 | MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
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480 | end |
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481 | end |
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482 | case 'grid' %case of fields defined on a structured grid |
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483 | FFName=''; |
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484 | if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) |
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485 | FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable |
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486 | MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) |
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487 | MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; |
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488 | MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; |
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489 | end |
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490 | % select good data on each view |
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491 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
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492 | VarName=Data{1}.ListVarName{ivar}; |
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493 | for iview=1:NbView |
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494 | if isempty(FFName) |
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495 | check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else |
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496 | else |
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497 | check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else |
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498 | end |
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499 | Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
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500 | if iview==1 |
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501 | %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field |
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502 | MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
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503 | NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point |
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504 | elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) |
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505 | errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; |
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506 | return |
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507 | else |
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508 | MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data |
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509 | NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else |
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510 | end |
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511 | end |
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512 | MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point |
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513 | MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data |
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514 | end |
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515 | end |
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516 | end |
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517 | end |
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