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 2008-2018, 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=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': one output file per input file index, '=NbInput_i': one file per input file index i, '=NbSlice': one file per slice
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73 | % check for selection of a projection object
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74 | hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series
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75 | if ~isfield(Param,'ProjObject')
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76 | answer=msgbox_uvmat('INPUT_Y-N','use a projection object?');
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77 | if strcmp(answer,'Yes')
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78 | hhseries=guidata(hseries);
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79 | set(hhseries.CheckObject,'Visible','on')
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80 | set(hhseries.CheckObject,'Value',1)
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81 | Param.CheckObject=1;
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82 | series('CheckObject_Callback',hseries,[],hhseries); %file input with xml reading in uvmat, show the image in phys coordinates
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83 | end
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84 | end
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85 | % introduce bin size for histograms
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86 | if isfield(Param,'CheckObject') && Param.CheckObject
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87 | SeriesData=get(hseries,'UserData');
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88 | if ismember(SeriesData.ProjObject.ProjMode,{'inside','outside'})
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89 | answer=msgbox_uvmat('INPUT_TXT','set bin size for histograms (or keep ''auto'' by default)?','auto');
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90 | ParamOut.ActionInput.VarMesh=str2num(answer);
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91 | end
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92 | end
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93 | % check the existence of the first and last file in the series
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94 | first_j=[];
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95 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
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96 | last_j=[];
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97 | if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
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98 | PairString='';
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99 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
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100 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
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101 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
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102 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
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103 | if ~exist(FirstFileName,'file')
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104 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
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105 | else
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106 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
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107 | LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
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108 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
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109 | if ~exist(LastFileName,'file')
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110 | msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
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111 | end
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112 | end
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113 | % determine volume scan mode
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114 | prompt = {'volume scan mode (Yes/No)'};
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115 | dlg_title = 'determine volume scan';
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116 | num_lines= 1;
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117 | def = { 'No'};
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118 | answer=msgbox_uvmat('INPUT_Y-N','volume scan mode (OK/No)?');
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119 | % answer = inputdlg(prompt,dlg_title,num_lines,def);
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120 | if isempty(answer)
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121 | return
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122 | end
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123 | %check input consistency
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124 | if strcmp(answer,'Yes')
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125 | ParamOut.NbSlice=1;% set NbSlice to 1 ( for i index)
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126 | ParamOut.ActionInput.CheckVolume=1;
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127 | end
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128 | return
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129 | end
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130 |
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131 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%%
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132 | ParamOut=[];%default output
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133 | %% read input parameters from an xml file if input is a file name (batch mode)
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134 | checkrun=1;
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135 | if ischar(Param)
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136 | Param=xml2struct(Param);% read Param as input file (batch case)
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137 | checkrun=0;
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138 | end
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139 | hseries=findobj(allchild(0),'Tag','series');
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140 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
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141 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
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142 |
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143 | %% define the directory for result file (with path=RootPath{1})
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144 | OutputDir=[Param.OutputSubDir Param.OutputDirExt];
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145 |
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146 | %% root input file(s) name, type and index series
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147 | RootPath=Param.InputTable(:,1);
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148 | RootFile=Param.InputTable(:,3);
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149 | SubDir=Param.InputTable(:,2);
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150 | NomType=Param.InputTable(:,4);
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151 | FileExt=Param.InputTable(:,5);
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152 |
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153 | hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
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154 | % gives the series of input file names and indices set by the input parameters:
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155 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
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156 | % filecell{iview,fileindex}:
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157 | % iview: line in the table corresponding to a given file series
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158 | % fileindex: file index with i and j reshaped as a 1D array
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159 | % 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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160 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
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161 | if ~isempty(hdisp),delete(hdisp),end;%end the waiting display
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162 |
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163 | NbView=numel(i1_series);%number of input file series (lines in InputTable)
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164 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
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165 | NbField_i=size(i1_series{1},2); %nb of fields for the i index
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166 | NbField=NbField_j*NbField_i; %total number of fields
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167 |
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168 | %% determine the file type on each line from the first input file
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169 | NcTypeOptions={'netcdf','civx','civdata'};
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170 | for iview=1:NbView
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171 | if ~exist(filecell{iview,1}','file')
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172 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
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173 | return
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174 | end
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175 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
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176 | FileType{iview}=FileInfo{iview}.FileType;
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177 | CheckImage{iview}=strcmp(FileInfo{iview}.FieldType,'image');% =1 for images
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178 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
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179 | if ~isempty(j1_series{iview})
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180 | frame_index{iview}=j1_series{iview};
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181 | else
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182 | frame_index{iview}=i1_series{iview};
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183 | end
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184 | end
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185 |
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186 | %% calibration data and timing: read the ImaDoc files
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187 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
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188 | if size(time,1)>1
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189 | diff_time=max(max(diff(time)));
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190 | if diff_time>0
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191 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
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192 | end
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193 | end
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194 |
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195 | %% coordinate transform or other user defined transform
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196 | transform_fct='';%default
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197 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
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198 | addpath(Param.FieldTransform.TransformPath)
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199 | transform_fct=str2func(Param.FieldTransform.TransformName);
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200 | rmpath(Param.FieldTransform.TransformPath)
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201 | if isfield(Param,'TransformInput')
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202 | XmlData{1}.TransformInput=Param.TransformInput;
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203 | end
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204 | end
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205 |
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206 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%%
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207 | % EDIT FROM HERE
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208 |
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209 | %% check the validity of input file types and set the output file type
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210 | if CheckImage{1}
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211 | FileExtOut='.png'; % write result as .png images for image inputs
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212 | elseif CheckNc{1}
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213 | FileExtOut='.nc';% write result as .nc files for netcdf inputs
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214 | else
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215 | disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
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216 | return
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217 | end
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218 | if NbView==2 && ~isequal(CheckImage{1},CheckImage{2})
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219 | disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
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220 | return
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221 | end
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222 | if isfield(Param,'ProjObject') && ~strcmp(Param.ProjObject.Type,'plane')
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223 | FileExtOut='.nc';% write result as .nc files (even for image input)
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224 | end
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225 |
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226 | %% settings for the output file
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227 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
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228 | first_i=i1_series{1}(1);
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229 | last_i=i1_series{1}(end);
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230 | if isempty(j1_series{1})% if there is no second index j
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231 | first_j=1;last_j=1;
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232 | else
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233 | first_j=j1_series{1}(1);
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234 | last_j=j1_series{1}(end);
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235 | end
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236 |
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237 | %% Set field names and velocity types
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238 | InputFields{1}=[];%default (case of images)
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239 | if NbView==2
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240 | InputFields{2}=[];%default (case of images)
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241 | end
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242 | if isfield(Param,'InputFields')
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243 | InputFields{1}=Param.InputFields;
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244 | if NbView==2
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245 | InputFields{2}=Param.InputFields;%default
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246 | if isfield(Param.InputFields,'FieldName_1')
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247 | InputFields{2}.FieldName=Param.InputFields.FieldName_1;
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248 | if isfield(Param.InputFields,'VelType_1')
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249 | InputFields{2}.VelType=Param.InputFields.VelType_1;
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250 | end
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251 | end
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252 | end
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253 | end
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254 |
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255 | VarMesh=[];
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256 | if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
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257 | if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms
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258 | VarMesh=Param.ActionInput.VarMesh;
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259 | else
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260 | VarMesh=[];
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261 | disp_uvmat('WARNING','automatic bin size for histograms, select aver_stat again to set the value',checkrun)
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262 | end
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263 | end
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264 |
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265 | NbSlice_j=1;% number of j slices =1 except fo volume scan
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266 | index_series=1:size(filecell,2);
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267 | index_j=1;
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268 |
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269 | %% set volume scan if requested
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270 | first_j_out=first_j;%first j index to use for the output file name
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271 | last_j_out=last_j;%last j index to use for the output file name
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272 | if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'CheckVolume') ...
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273 | && Param.ActionInput.CheckVolume
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274 | index_j=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j;
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275 | NbSlice_j=numel(index_j);
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276 | index_series=1:NbSlice_j:size(filecell,2);
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277 | end
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278 |
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279 | %% loop on j slices (volume scan)
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280 | for islice=index_j
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281 | nbfiles=0;%counter of the successfully read files (bad files are skipped)
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282 | if NbSlice_j>1
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283 | first_j_out=islice;%first and last j index to use for the output file name are the current j index
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284 | last_j_out=islice;
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285 | end
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286 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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287 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
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288 | for index=index_series+index_j(islice)-index_j(1)
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289 | update_waitbar(WaitbarHandle,index/NbField)
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290 | if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
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291 | disp('program stopped by user')
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292 | break
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293 | end
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294 |
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295 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
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296 | for iview=1:NbView
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297 | % reading input file(s)
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298 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
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299 | if ~isempty(errormsg)
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300 | errormsg=['error of input reading: ' errormsg];
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301 | break% leave the loop on views in case of error
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302 | end
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303 | if ~isempty(NbSlice_calib)
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304 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
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305 | end
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306 | end
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307 | %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
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308 |
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309 | if ~isempty(errormsg)
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310 | disp(errormsg)
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311 | continue % go to next input field in case of error (file skipped in the average)
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312 | end
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313 | Field=Data{1}; % default input field structure
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314 | nbfiles=nbfiles+1; %increment the file counter
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315 |
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316 | %% coordinate transform (or other user defined transform)
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317 | if ~isempty(transform_fct)
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318 | switch nargin(transform_fct)
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319 | case 4
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320 | if length(Data)==2
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321 | Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
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322 | else
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323 | Field=transform_fct(Data{1},XmlData{1});
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324 | end
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325 | case 3
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326 | if length(Data)==2
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327 | Field=transform_fct(Data{1},XmlData{1},Data{2});
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328 | else
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329 | Field=transform_fct(Data{1},XmlData{1});
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330 | end
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331 | case 2
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332 | Field=transform_fct(Data{1},XmlData{1});
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333 | case 1
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334 | Field=transform_fct(Data{1});
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335 | end
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336 | end
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337 |
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338 | %% field projection on an object
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339 | if Param.CheckObject
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340 | if strcmp(Param.ProjObject.ProjMode,'interp_tps')
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341 | Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed
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342 | end
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343 | [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh);
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344 | if ~isempty(errormsg)
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345 | disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun)
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346 | return
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347 | end
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348 | end
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349 |
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350 | %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%%
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351 | if nbfiles==1 %first field
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352 | time_1=[];
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353 | if isfield(Field,'Time')
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354 | time_1=Field.Time(1);
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355 | end
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356 | DataOut=Field;%outcome reproduces the first (projected) field by default
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357 | DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files
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358 | if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms
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359 | for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram)
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360 | VarName=Field.ListVarName{ivar};
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361 | if isfield(Data{1},VarName)
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362 | DataOut.(VarName)=Field.(VarName);
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363 | DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName)));
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364 | VarMesh=DataOut.(VarName)(2)-DataOut.(VarName)(1);
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365 | end
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366 | end
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367 | disp(['mesh for histogram = ' num2str(VarMesh)])
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368 | else
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369 | errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable
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370 | if isfield(Field,'VarAttribute')
|
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371 | for ivar=1:numel(Field.ListVarName)
|
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372 | VarName=Field.ListVarName{ivar};
|
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373 | DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
|
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374 | NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
|
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375 |
|
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376 | for iivar=1:length(Field.VarAttribute)
|
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377 | if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')...
|
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378 | && strcmp(Field.VarAttribute{iivar}.Role,'errorflag')
|
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379 | errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar
|
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380 | end
|
---|
381 | end
|
---|
382 | end
|
---|
383 | DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result
|
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384 | DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result
|
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385 | DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result
|
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386 | else
|
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387 | for ivar=1:numel(Field.ListVarName)
|
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388 | VarName=Field.ListVarName{ivar};
|
---|
389 | DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
|
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390 | NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
|
---|
391 | end
|
---|
392 | end
|
---|
393 |
|
---|
394 | end
|
---|
395 | end %current field
|
---|
396 | for ivar=1:length(DataOut.ListVarName)
|
---|
397 | VarName=DataOut.ListVarName{ivar};
|
---|
398 | sizmean=size(DataOut.(VarName));
|
---|
399 | siz=size(Field.(VarName));
|
---|
400 | if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
|
---|
401 | if isfield(Data{1},VarName)
|
---|
402 | MaxValue=max(DataOut.(VarName));% current max of histogram absissa
|
---|
403 | MinValue=min(DataOut.(VarName));% current min of histogram absissa
|
---|
404 | % VarMesh=Field.VarAttribute{ivar}.Mesh;
|
---|
405 | MaxIndex=round(MaxValue/VarMesh);
|
---|
406 | MinIndex=round(MinValue/VarMesh);
|
---|
407 | MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field
|
---|
408 | MinIndex_new=round(min(Field.(VarName)/VarMesh));
|
---|
409 | if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one
|
---|
410 | DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values
|
---|
411 | DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_new-MaxIndex)]; % append the new histo values
|
---|
412 | end
|
---|
413 | if MinIndex_new <= MinIndex-1
|
---|
414 | DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values
|
---|
415 | DataOut.([VarName 'Histo'])=[zeros(1,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values
|
---|
416 | ind_start=1;
|
---|
417 | else
|
---|
418 | ind_start=MinIndex_new-MinIndex+1;
|
---|
419 | end
|
---|
420 | DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)=...
|
---|
421 | DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']);
|
---|
422 | end
|
---|
423 | elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
|
---|
424 | disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid'],checkrun)
|
---|
425 | return
|
---|
426 | else
|
---|
427 | if errorvar(ivar)==0
|
---|
428 | check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else
|
---|
429 | else
|
---|
430 | check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else
|
---|
431 | end
|
---|
432 | Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
|
---|
433 | DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
|
---|
434 | NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point
|
---|
435 | end
|
---|
436 | end
|
---|
437 | %%%%%%%%%%%% END MAIN RUNNING OPERATIONS %%%%%%%%%%%%
|
---|
438 | end
|
---|
439 | %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
|
---|
440 |
|
---|
441 | if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}))
|
---|
442 | for ivar=1:length(Field.ListVarName)
|
---|
443 | VarName=Field.ListVarName{ivar};
|
---|
444 | DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean
|
---|
445 | end
|
---|
446 | end
|
---|
447 | nbmissing=numel(index_series+index_j(islice)-index_j(1))-nbfiles;
|
---|
448 | if nbmissing~=0
|
---|
449 | if NbSlice_j==1
|
---|
450 | disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun)
|
---|
451 | else
|
---|
452 | disp(['WARNING: ' num2str(nbmissing) ' input files are missing or skipped in slice ' num2str(islice)])
|
---|
453 | end
|
---|
454 | end
|
---|
455 | if isempty(time) % time is read from files
|
---|
456 | if isfield(Field,'Time')
|
---|
457 | time_end=Field.Time(1);%last time read
|
---|
458 | if ~isempty(time_1)
|
---|
459 | DataOut.Time=time_1;
|
---|
460 | DataOut.Time_end=time_end;
|
---|
461 | end
|
---|
462 | end
|
---|
463 | else % time from ImaDoc prevails if it exists
|
---|
464 | DataOut.Time=time(1);
|
---|
465 | DataOut.Time_end=time(end);
|
---|
466 | end
|
---|
467 |
|
---|
468 | %% writing the result file
|
---|
469 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
|
---|
470 | if strcmp(FileExtOut,'.png') %case of images
|
---|
471 | if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
|
---|
472 | DataOut.A=uint16(DataOut.A);
|
---|
473 | imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
|
---|
474 | else
|
---|
475 | DataOut.A=uint8(DataOut.A);
|
---|
476 | imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
|
---|
477 | end
|
---|
478 | disp([OutputFile ' written']);
|
---|
479 | else %case of netcdf file , determine global attributes
|
---|
480 | errormsg=struct2nc(OutputFile,DataOut); %save result file
|
---|
481 | if isempty(errormsg)
|
---|
482 | disp([OutputFile ' written']);
|
---|
483 | else
|
---|
484 | disp(['error in writting result file: ' errormsg])
|
---|
485 | end
|
---|
486 | end % end averaging loop
|
---|
487 | end
|
---|
488 |
|
---|
489 | %% open the result file with uvmat (in RUN mode)
|
---|
490 | if checkrun
|
---|
491 | uvmat(OutputFile)% open the last result file with uvmat
|
---|
492 | end
|
---|