1 | %'filter_time': apply a a sliding filter in a time series |
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2 | %------------------------------------------------------------------------ |
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3 | % function ParamOut=filter_time(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, (several5.804 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 | % 900 |
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28 | % .IndexRange: set the file or frame indices on which the action must be performseriesed |
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29 | % .FieldTransform: .TransformName: name of the select39ed 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 | % uvmat .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 | % Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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42 | % http://www.legi.grenoble-inp.fr |
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43 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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44 | % |
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45 | % This file is part of the toolbox UVMAT. |
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46 | % |
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47 | % UVMAT is free software; you can redistribute it and/or modify |
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48 | % it under the terms of the GNU General Public License as published |
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49 | % by the Free Software Foundation; either version 2 of the license, |
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50 | % or (at your option) any later version. |
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51 | % |
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52 | % UVMAT is distributed in the hope that it will be useful, |
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53 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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54 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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55 | % GNU General Public License (see LICENSE.txt) for more details. |
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56 | %======================================================================= |
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57 | |
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58 | function ParamOut=filter_time(Param) |
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59 | |
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60 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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61 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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62 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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63 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to mseriesax (options 'off'/'on', 'off' by default) |
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64 | ParamOut.NbSlice=1; %nbre of slices ('off' by default) |
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65 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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66 | ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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67 | ParamOut.FieldTransform = 'off';%can use a transform function |
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68 | ParamOut.ProjObject='off';%can use projection object39(option 'off'/'on', |
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69 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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70 | ParamOut.OutputDirExt='.tfilter';%set the output dir extension |
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71 | 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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72 | |
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73 | %% check the first input 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 | PairString=''; |
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77 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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78 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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79 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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80 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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81 | if exist(FirstFileName,'file') |
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82 | FileInfo=get_file_info(FirstFileName); |
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83 | if ~(isfield(FileInfo,'FileType')&& strcmp(FileInfo.FileType,'netcdf')) |
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84 | msgbox_uvmat('ERROR','this fct works only on netcdf files (fields projected on a grid, notraw civ data)') |
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85 | return |
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86 | end |
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87 | else |
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88 | msgbox_uvmat('ERROR',['the input file ' FirstFileName ' does not exist']) |
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89 | return |
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90 | end |
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91 | |
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92 | %% setting the fltering window length |
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93 | answer = msgbox_uvmat('INPUT_TXT','set the filering window length','3'); |
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94 | ParamOut.ActionInput.WindowLength=str2double(answer); |
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95 | return |
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96 | end |
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97 | |
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98 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% |
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99 | ParamOut=[];%default output |
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100 | %% read input parameters from an xml file if input is a file name (batch mode) |
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101 | checkrun=1; |
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102 | if ischar(Param) |
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103 | Param=xml2struct(Param);% read Param as input file (batch case) |
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104 | checkrun=0; |
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105 | end |
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106 | |
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107 | hseries=findobj(allchild(0),'Tag','series'); |
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108 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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109 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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110 | |
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111 | |
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112 | %% root input file(s) name, type and index series |
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113 | RootPath=Param.InputTable(:,1); |
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114 | RootFile=Param.InputTable(:,3); |
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115 | SubDir=Param.InputTable(:,2); |
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116 | NomType=Param.InputTable(:,4); |
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117 | FileExt=Param.InputTable(:,5); |
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118 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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119 | %%%%%%%%%%%% |
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120 | % The cell array filecell is the list of input file names, while |
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121 | % filecell{iview,fileindex}: |
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122 | % iview: line in the table corresponding to a given file series |
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123 | % fileindex: file index within the file series, |
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124 | % 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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125 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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126 | %%%%%%%%%%%% NbView=1 : a single input series |
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127 | |
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128 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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129 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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130 | NbField=NbField_j*NbField_i; %total number of fields |
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131 | |
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132 | %% define the output file (unique for the whole series) |
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133 | OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); |
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134 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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135 | first_j=[];last_j=[];% %% check the first input file in the series |
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136 | |
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137 | PairString=''; |
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138 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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139 | |
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140 | |
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141 | % OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device)); |
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142 | % RootFileOut=RootFile{1}; |
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143 | % NomTypeOut='_1'; |
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144 | |
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145 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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146 | disp('loop for filtering started') |
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147 | |
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148 | for index=1:NbField |
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149 | index |
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150 | |
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151 | Field= read_field(filecell{1,index},'netcdf',Param.InputFields); |
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152 | |
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153 | %%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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154 | if index==1 %first field, initialisation output data |
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155 | |
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156 | DataOut.ListGlobalAttribute= {'Conventions','Time'}; |
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157 | DataOut.Conventions='uvmat'; |
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158 | %DataOut.ListVarName={'coord_y','coord_x','Ufilter','Vfilter','Wfilter'}; |
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159 | ListFields=Param.InputFields.FieldName; |
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160 | YName=Param.InputFields.Coord_y; |
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161 | XName=Param.InputFields.Coord_x; |
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162 | NbField=numel(ListFields); |
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163 | for ilist=1:NbField |
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164 | ListFilter{ilist}=[ListFields{ilist} '_filter']; |
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165 | VarDimName{ilist}={YName,XName}; |
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166 | end |
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167 | DataOut.ListVarName=[{YName,XName} ListFilter]; |
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168 | DataOut.VarDimName=[{YName,XName} VarDimName]; |
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169 | npy=numel(Field.(YName)); |
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170 | npx=numel(Field.(XName)); |
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171 | DataOut.(XName)=Field.(XName); |
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172 | DataOut.(YName)=Field.(YName); |
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173 | TimeBlock=zeros(Param.ActionInput.WindowLength,1); |
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174 | |
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175 | UVblock=zeros(Param.ActionInput.WindowLength,NbField,npy,npx); |
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176 | % Vblock=zeros(Param.ActionInput.WindowLength,npy,npx); |
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177 | % Wblock=zeros(Param.ActionInput.WindowLength,npy,npx); |
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178 | end |
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179 | TimeBlock=circshift(TimeBlock,[-1 0 ]); |
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180 | UVblock=circshift(UVblock,[-1 0 0 0]); %shift U by ishift along the first index |
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181 | % Vblock=circshift(Vblock,[-1 0 0 0]); %shift U by ishift along the first index |
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182 | % Wblock=circshift(Wblock,[-1 0 0]); %shift U by ishift along the first index |
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183 | TimeBlock(end)=Field.Time; |
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184 | for ilist=1:NbField |
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185 | UVblock(end,ilist,:,:)=Field.(ListFields{ilist}); |
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186 | end |
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187 | % Vblock(end,:,:)=Field.V; |
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188 | % Vblock(end,:,:)=Field.W; |
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189 | sumindex=min(index,Param.ActionInput.WindowLength)-1; |
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190 | DataOut.Timefilter=mean(TimeBlock(end-sumindex:end,:));%mid time |
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191 | for ilist=1:NbField |
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192 | DataOut.(ListFilter{ilist})=squeeze(mean(UVblock(end-sumindex:end,ilist,:,:),1,'omitnan')); |
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193 | end |
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194 | % DataOut.Vfilter=squeeze(mean(Vblock(end-sumindex:end,:,:),1,'omitnan')); |
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195 | % DataOut.Wfilter=squeeze(mean(Wblock(end-sumindex:end,:,:),1,'omitnan')); |
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196 | %updating output the netcdf file |
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197 | [i1,i2,j1,j2] = get_file_index(i1_series{1}(index),[],PairString{1}); |
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198 | OutputFile=fullfile_uvmat(OutputPath,OutputDir,Param.InputTable{1,3},'.nc',NomType{1},i1,i2,j1,j2); |
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199 | errormsg=struct2nc(OutputFile, DataOut); |
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200 | if isempty(errormsg) |
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201 | disp([OutputFile ' written']) |
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202 | else |
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203 | disp(errormsg) |
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204 | end |
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205 | end |
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206 | % writing the result file as netcdf file |
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207 | % i1=i1_series{1}(index)-ceil(NpTime/2); |
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208 | % OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeOut,i1); |
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209 | |
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210 | 'END' |
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