1 | %'aver_stat': calculate field average over a time series |
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2 | %------------------------------------------------------------------------ |
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3 | % function ParamOut=aver_stat(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 2008-2014, LEGI UMR 5519 / CNRS UJF 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=aver_stat(Param) |
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60 | |
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61 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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62 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
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63 | ParamOut.AllowInputSort='off';% 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='on'; %nbre of slices ('off' by default) |
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66 | ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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67 | ParamOut.FieldName='two';% 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.ProjObject='on';%can use projection object(option 'off'/'on', |
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70 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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71 | ParamOut.OutputDirExt='.stat';%set the output dir extension |
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72 | 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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73 | % check the existence of the first file in the series |
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74 | first_j=[]; |
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75 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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76 | last_j=[]; |
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77 | if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_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 | else |
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86 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); |
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87 | LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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88 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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89 | if ~exist(FirstFileName,'file') |
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90 | msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) |
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91 | end |
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92 | end |
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93 | return |
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94 | end |
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95 | |
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96 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% |
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97 | ParamOut=[];%default output |
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98 | %% read input parameters from an xml file if input is a file name (batch mode) |
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99 | checkrun=1; |
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100 | if ischar(Param) |
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101 | Param=xml2struct(Param);% read Param as input file (batch case) |
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102 | checkrun=0; |
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103 | end |
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104 | hseries=findobj(allchild(0),'Tag','series'); |
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105 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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106 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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107 | |
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108 | %% define the directory for result file (with path=RootPath{1}) |
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109 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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110 | |
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111 | %% root input file(s) name, type and index series |
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112 | RootPath=Param.InputTable(:,1); |
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113 | RootFile=Param.InputTable(:,3); |
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114 | SubDir=Param.InputTable(:,2); |
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115 | NomType=Param.InputTable(:,4); |
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116 | FileExt=Param.InputTable(:,5); |
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117 | hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); |
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118 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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119 | if ~isempty(hdisp),delete(hdisp),end; |
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120 | %%%%%%%%%%%% |
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121 | % The cell array filecell is the list of input file names, while |
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122 | % filecell{iview,fileindex}: |
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123 | % iview: line in the table corresponding to a given file series |
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124 | % fileindex: file index within the file series, |
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125 | % 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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126 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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127 | %%%%%%%%%%%% |
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128 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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129 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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130 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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131 | NbField=NbField_j*NbField_i; %total number of fields |
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132 | |
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133 | %% determine the file type on each line from the first input file |
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134 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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135 | NcTypeOptions={'netcdf','civx','civdata'}; |
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136 | for iview=1:NbView |
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137 | if ~exist(filecell{iview,1}','file') |
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138 | msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) |
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139 | return |
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140 | end |
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141 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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142 | FileType{iview}=FileInfo{iview}.FileType; |
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143 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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144 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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145 | if ~isempty(j1_series{iview}) |
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146 | frame_index{iview}=j1_series{iview}; |
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147 | else |
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148 | frame_index{iview}=i1_series{iview}; |
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149 | end |
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150 | end |
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151 | |
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152 | %% calibration data and timing: read the ImaDoc files |
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153 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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154 | if size(time,1)>1 |
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155 | diff_time=max(max(diff(time))); |
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156 | if diff_time>0 |
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157 | msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) |
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158 | end |
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159 | end |
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160 | |
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161 | %% coordinate transform or other user defined transform |
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162 | transform_fct='';%default |
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163 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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164 | addpath(Param.FieldTransform.TransformPath) |
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165 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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166 | rmpath(Param.FieldTransform.TransformPath) |
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167 | end |
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168 | |
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169 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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170 | % EDIT FROM HERE |
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171 | |
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172 | %% check the validity of input file types |
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173 | if CheckImage{1} |
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174 | FileExtOut='.png'; % write result as .png images for image inputs |
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175 | elseif CheckNc{1} |
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176 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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177 | else |
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178 | msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) |
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179 | return |
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180 | end |
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181 | if NbView==2 && ~isequal(CheckImage{1},CheckImage{2}) |
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182 | msgbox_uvmat('ERROR','input must be two image series or two netcdf file series') |
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183 | return |
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184 | end |
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185 | |
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186 | %% settings for the output file |
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187 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file |
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188 | first_i=i1_series{1}(1); |
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189 | last_i=i1_series{1}(end); |
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190 | if isempty(j1_series{1})% if there is no second index j |
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191 | first_j=1;last_j=1; |
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192 | else |
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193 | first_j=j1_series{1}(1); |
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194 | last_j=j1_series{1}(end); |
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195 | end |
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196 | |
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197 | %% Set field names and velocity types |
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198 | InputFields{1}=[];%default (case of images) |
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199 | if isfield(Param,'InputFields') |
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200 | InputFields{1}=Param.InputFields; |
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201 | end |
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202 | if NbView==2 |
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203 | InputFields{2}=[];%default (case of images) |
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204 | if isfield(Param,'InputFields') |
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205 | InputFields{2}=Param.InputFields{1};%default |
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206 | if isfield(Param.InputFields,'FieldName_1') |
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207 | InputFields{2}.FieldName=Param.InputFields.FieldName_1; |
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208 | if isfield(Param.InputFields,'VelType_1') |
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209 | InputFields{2}.VelType=Param.InputFields.VelType_1; |
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210 | end |
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211 | end |
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212 | end |
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213 | end |
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214 | |
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215 | % for i_slice=1:NbSlice |
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216 | % index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice |
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217 | nbfiles=0; |
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218 | nbmissing=0; |
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219 | |
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220 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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221 | for index=1:NbField |
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222 | update_waitbar(WaitbarHandle,index/NbField) |
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223 | if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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224 | disp('program stopped by user') |
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225 | break |
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226 | end |
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227 | |
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228 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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229 | for iview=1:NbView |
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230 | % reading input file(s) |
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231 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); |
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232 | if ~isempty(errormsg) |
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233 | errormsg=['error of input reading: ' errormsg]; |
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234 | break |
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235 | end |
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236 | if ~isempty(NbSlice_calib) |
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237 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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238 | end |
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239 | end |
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240 | %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%% |
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241 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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242 | % EDIT FROM HERE |
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243 | |
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244 | if isempty(errormsg) |
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245 | Field=Data{1}; % default input field structure |
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246 | %% coordinate transform (or other user defined transform) |
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247 | if ~isempty(transform_fct) |
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248 | switch nargin(transform_fct) |
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249 | case 4 |
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250 | if length(Data)==2 |
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251 | Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); |
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252 | else |
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253 | Field=transform_fct(Data{1},XmlData{1}); |
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254 | end |
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255 | case 3 |
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256 | if length(Data)==2 |
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257 | Field=transform_fct(Data{1},XmlData{1},Data{2}); |
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258 | else |
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259 | Field=transform_fct(Data{1},XmlData{1}); |
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260 | end |
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261 | case 2 |
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262 | Field=transform_fct(Data{1},XmlData{1}); |
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263 | case 1 |
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264 | Field=transform_fct(Data{1}); |
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265 | end |
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266 | end |
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267 | |
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268 | %% calculate tps coefficients if needed |
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269 | if isfield(Param,'ProjObject')&&isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps') |
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270 | Field=tps_coeff_field(Field,check_proj_tps); |
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271 | end |
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272 | |
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273 | %field projection on an object |
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274 | if Param.CheckObject |
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275 | [Field,errormsg]=proj_field(Field,Param.ProjObject); |
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276 | if ~isempty(errormsg) |
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277 | msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg]) |
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278 | return |
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279 | end |
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280 | end |
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281 | nbfiles=nbfiles+1; |
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282 | |
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283 | %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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284 | if nbfiles==1 %first field |
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285 | time_1=[]; |
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286 | if isfield(Field,'Time') |
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287 | time_1=Field.Time(1); |
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288 | end |
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289 | DataOut=Field;%default |
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290 | DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files |
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291 | for ivar=1:length(Field.ListVarName) |
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292 | VarName=Field.ListVarName{ivar}; |
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293 | DataOut.(VarName)=double(DataOut.(VarName)); |
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294 | end |
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295 | else %current field |
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296 | for ivar=1:length(Field.ListVarName) |
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297 | VarName=Field.ListVarName{ivar}; |
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298 | sizmean=size(DataOut.(VarName)); |
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299 | siz=size(Field.(VarName)); |
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300 | if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean) |
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301 | disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid'],checkrun) |
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302 | return |
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303 | else |
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304 | DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum |
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305 | end |
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306 | end |
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307 | end |
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308 | %%%%%%%%%%%% END MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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309 | else |
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310 | disp(errormsg) |
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311 | end |
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312 | end |
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313 | %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% |
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314 | |
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315 | for ivar=1:length(Field.ListVarName) |
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316 | VarName=Field.ListVarName{ivar}; |
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317 | DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean |
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318 | end |
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319 | if nbmissing~=0 |
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320 | msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted']) |
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321 | end |
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322 | if isempty(time) % time is read from files |
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323 | if isfield(Field,'Time') |
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324 | time_end=Field.Time(1);%last time read |
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325 | if ~isempty(time_1) |
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326 | DataOut.Time=time_1; |
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327 | DataOut.Time_end=time_end; |
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328 | end |
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329 | end |
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330 | else % time from ImaDoc prevails if it exists |
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331 | DataOut.Time=time(1); |
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332 | DataOut.Time_end=time(end); |
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333 | end |
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334 | |
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335 | %% writing the result file |
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336 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); |
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337 | if CheckImage{1} %case of images |
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338 | if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16)) |
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339 | DataOut.A=uint16(DataOut.A); |
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340 | imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images |
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341 | else |
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342 | DataOut.A=uint8(DataOut.A); |
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343 | imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images |
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344 | end |
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345 | disp([OutputFile ' written']); |
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346 | else %case of netcdf input file , determine global attributes |
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347 | errormsg=struct2nc(OutputFile,DataOut); %save result file |
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348 | if isempty(errormsg) |
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349 | disp([OutputFile ' written']); |
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350 | else |
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351 | disp(['error in writting result file: ' errormsg]) |
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352 | end |
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353 | end % end averaging loop |
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354 | |
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355 | %% open the result file with uvmat (in RUN mode) |
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356 | if checkrun |
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357 | uvmat(OutputFile)% open the last result file with uvmat |
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358 | end |
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