[573] | 1 | %'aver_stat': calculate field average over a time series |
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[169] | 2 | %------------------------------------------------------------------------ |
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[457] | 3 | % function ParamOut=aver_stat(Param) |
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[169] | 4 | % |
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[447] | 5 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[457] | 6 | % |
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[169] | 7 | %OUTPUT |
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[596] | 8 | % ParamOut: sets options in the GUI series.fig needed for the function |
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[169] | 9 | % |
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| 10 | %INPUT: |
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[447] | 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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[596] | 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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[169] | 15 | % |
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[596] | 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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[447] | 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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[474] | 21 | % .OutputDirExt: directory extension for data outputs |
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[447] | 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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[596] | 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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[447] | 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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[596] | 32 | % .FieldName: name(s) of the field |
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[447] | 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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[596] | 36 | % .Coord_y: name of y coordinate variable |
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| 37 | % .Coord_x: name of x coordinate variable |
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[447] | 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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[810] | 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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[457] | 59 | function ParamOut=aver_stat(Param) |
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[447] | 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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[716] | 62 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
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[605] | 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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[592] | 71 | ParamOut.OutputDirExt='.stat';%set the output dir extension |
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[605] | 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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[871] | 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 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=str2double(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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[716] | 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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[871] | 109 | if ~exist(LastFileName,'file') |
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[716] | 110 | msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) |
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| 111 | end |
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[605] | 112 | end |
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| 113 | return |
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[27] | 114 | end |
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| 115 | |
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[474] | 116 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% |
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[624] | 117 | ParamOut=[];%default output |
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[592] | 118 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 119 | checkrun=1; |
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[457] | 120 | if ischar(Param) |
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[592] | 121 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 122 | checkrun=0; |
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[361] | 123 | end |
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[624] | 124 | hseries=findobj(allchild(0),'Tag','series'); |
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| 125 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 126 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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[592] | 127 | |
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[624] | 128 | %% define the directory for result file (with path=RootPath{1}) |
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[474] | 129 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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| 130 | |
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[609] | 131 | %% root input file(s) name, type and index series |
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[457] | 132 | RootPath=Param.InputTable(:,1); |
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| 133 | RootFile=Param.InputTable(:,3); |
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| 134 | SubDir=Param.InputTable(:,2); |
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| 135 | NomType=Param.InputTable(:,4); |
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| 136 | FileExt=Param.InputTable(:,5); |
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[751] | 137 | hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); |
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[374] | 138 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[751] | 139 | if ~isempty(hdisp),delete(hdisp),end; |
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[474] | 140 | %%%%%%%%%%%% |
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| 141 | % The cell array filecell is the list of input file names, while |
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| 142 | % filecell{iview,fileindex}: |
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[447] | 143 | % iview: line in the table corresponding to a given file series |
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| 144 | % fileindex: file index within the file series, |
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| 145 | % 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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| 146 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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[474] | 147 | %%%%%%%%%%%% |
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[673] | 148 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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| 149 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 150 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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| 151 | NbField=NbField_j*NbField_i; %total number of fields |
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[43] | 152 | |
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[609] | 153 | %% determine the file type on each line from the first input file |
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[447] | 154 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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| 155 | NcTypeOptions={'netcdf','civx','civdata'}; |
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[673] | 156 | for iview=1:NbView |
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[451] | 157 | if ~exist(filecell{iview,1}','file') |
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[867] | 158 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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[451] | 159 | return |
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| 160 | end |
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[784] | 161 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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[783] | 162 | FileType{iview}=FileInfo{iview}.FileType; |
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[447] | 163 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 164 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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[454] | 165 | if ~isempty(j1_series{iview}) |
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| 166 | frame_index{iview}=j1_series{iview}; |
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| 167 | else |
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| 168 | frame_index{iview}=i1_series{iview}; |
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| 169 | end |
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[27] | 170 | end |
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| 171 | |
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[451] | 172 | %% calibration data and timing: read the ImaDoc files |
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[470] | 173 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 174 | if size(time,1)>1 |
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[27] | 175 | diff_time=max(max(diff(time))); |
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| 176 | if diff_time>0 |
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[867] | 177 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) |
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[27] | 178 | end |
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| 179 | end |
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| 180 | |
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[447] | 181 | %% coordinate transform or other user defined transform |
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| 182 | transform_fct='';%default |
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[478] | 183 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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[474] | 184 | addpath(Param.FieldTransform.TransformPath) |
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| 185 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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| 186 | rmpath(Param.FieldTransform.TransformPath) |
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[27] | 187 | end |
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[474] | 188 | |
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[447] | 189 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 190 | % EDIT FROM HERE |
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| 191 | |
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[871] | 192 | %% check the validity of input file types and set the output file type |
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[447] | 193 | if CheckImage{1} |
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| 194 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 195 | elseif CheckNc{1} |
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| 196 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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[635] | 197 | else |
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[867] | 198 | disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun) |
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[447] | 199 | return |
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| 200 | end |
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[673] | 201 | if NbView==2 && ~isequal(CheckImage{1},CheckImage{2}) |
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[867] | 202 | disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun) |
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[447] | 203 | return |
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| 204 | end |
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[871] | 205 | if isfield(Param,'ProjObject') && ~strcmp(Param.ProjObject.Type,'plane') |
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| 206 | FileExtOut='.nc';% write result as .nc files (even for image input) |
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| 207 | end |
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[635] | 208 | |
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| 209 | %% settings for the output file |
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[609] | 210 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file |
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[635] | 211 | first_i=i1_series{1}(1); |
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| 212 | last_i=i1_series{1}(end); |
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| 213 | if isempty(j1_series{1})% if there is no second index j |
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| 214 | first_j=1;last_j=1; |
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| 215 | else |
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| 216 | first_j=j1_series{1}(1); |
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| 217 | last_j=j1_series{1}(end); |
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| 218 | end |
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[442] | 219 | |
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[447] | 220 | %% Set field names and velocity types |
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| 221 | InputFields{1}=[];%default (case of images) |
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[869] | 222 | if NbView==2 |
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| 223 | InputFields{2}=[];%default (case of images) |
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| 224 | end |
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[447] | 225 | if isfield(Param,'InputFields') |
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| 226 | InputFields{1}=Param.InputFields; |
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[869] | 227 | if NbView==2 |
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| 228 | InputFields{2}=Param.InputFields;%default |
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[447] | 229 | if isfield(Param.InputFields,'FieldName_1') |
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| 230 | InputFields{2}.FieldName=Param.InputFields.FieldName_1; |
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| 231 | if isfield(Param.InputFields,'VelType_1') |
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| 232 | InputFields{2}.VelType=Param.InputFields.VelType_1; |
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| 233 | end |
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| 234 | end |
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[255] | 235 | end |
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| 236 | end |
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[871] | 237 | nbfiles=0;%counter of the successfully read files (bad files are skipped) |
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| 238 | VarMesh=NaN; |
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| 239 | if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})&& isfield(Param.ActionInput,'VarMesh')%case of histograms |
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| 240 | VarMesh=Param.ActionInput.VarMesh; |
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| 241 | end |
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[598] | 242 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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[673] | 243 | for index=1:NbField |
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| 244 | update_waitbar(WaitbarHandle,index/NbField) |
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[635] | 245 | if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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[624] | 246 | disp('program stopped by user') |
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| 247 | break |
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| 248 | end |
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| 249 | |
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[598] | 250 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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[673] | 251 | for iview=1:NbView |
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[598] | 252 | % reading input file(s) |
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| 253 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); |
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| 254 | if ~isempty(errormsg) |
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| 255 | errormsg=['error of input reading: ' errormsg]; |
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| 256 | break |
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[447] | 257 | end |
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[598] | 258 | if ~isempty(NbSlice_calib) |
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| 259 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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[526] | 260 | end |
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[598] | 261 | end |
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| 262 | %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%% |
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| 263 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 264 | % EDIT FROM HERE |
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[624] | 265 | |
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[598] | 266 | if isempty(errormsg) |
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| 267 | Field=Data{1}; % default input field structure |
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[871] | 268 | nbfiles=nbfiles+1; %increment the file counter |
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[598] | 269 | %% coordinate transform (or other user defined transform) |
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| 270 | if ~isempty(transform_fct) |
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| 271 | switch nargin(transform_fct) |
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| 272 | case 4 |
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| 273 | if length(Data)==2 |
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| 274 | Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); |
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| 275 | else |
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[526] | 276 | Field=transform_fct(Data{1},XmlData{1}); |
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[598] | 277 | end |
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| 278 | case 3 |
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| 279 | if length(Data)==2 |
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| 280 | Field=transform_fct(Data{1},XmlData{1},Data{2}); |
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| 281 | else |
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| 282 | Field=transform_fct(Data{1},XmlData{1}); |
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| 283 | end |
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| 284 | case 2 |
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| 285 | Field=transform_fct(Data{1},XmlData{1}); |
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| 286 | case 1 |
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| 287 | Field=transform_fct(Data{1}); |
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[255] | 288 | end |
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[598] | 289 | end |
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[624] | 290 | |
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[871] | 291 | %% field projection on an object |
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[598] | 292 | if Param.CheckObject |
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[871] | 293 | if strcmp(Param.ProjObject.ProjMode,'interp_tps') |
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| 294 | Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed |
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| 295 | end |
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| 296 | [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh); |
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[598] | 297 | if ~isempty(errormsg) |
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[867] | 298 | disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun) |
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[598] | 299 | return |
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[494] | 300 | end |
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[598] | 301 | end |
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[871] | 302 | |
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[598] | 303 | %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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| 304 | if nbfiles==1 %first field |
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| 305 | time_1=[]; |
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| 306 | if isfield(Field,'Time') |
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| 307 | time_1=Field.Time(1); |
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| 308 | end |
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[871] | 309 | DataOut=Field;%outcome reproduces the first (projected) field by default |
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| 310 | DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files |
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| 311 | if ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms |
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| 312 | for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram) |
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| 313 | VarName=Field.ListVarName{ivar}; |
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| 314 | if isfield(Data{1},VarName) |
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| 315 | DataOut.(VarName)=Field.(VarName); |
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| 316 | DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName))); |
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| 317 | VarMesh=DataOut.(VarName)(2)-DataOut.(VarName)(1); |
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[867] | 318 | end |
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| 319 | end |
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[871] | 320 | disp(['mesh for histogram = ' num2str(VarMesh)]) |
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| 321 | else |
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| 322 | errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable |
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| 323 | for ivar=1:numel(Field.ListVarName) |
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| 324 | VarName=Field.ListVarName{ivar}; |
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| 325 | DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero |
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| 326 | NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero |
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| 327 | for iivar=1:length(Field.VarAttribute) |
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| 328 | if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')... |
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| 329 | && strcmp(Field.VarAttribute{iivar}.Role,'errorflag') |
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| 330 | errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar |
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| 331 | end |
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| 332 | end |
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| 333 | end |
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| 334 | DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result |
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| 335 | DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result |
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| 336 | DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result |
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[598] | 337 | end |
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[867] | 338 | end %current field |
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| 339 | for ivar=1:length(DataOut.ListVarName) |
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[871] | 340 | VarName=DataOut.ListVarName{ivar}; |
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[867] | 341 | sizmean=size(DataOut.(VarName)); |
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| 342 | siz=size(Field.(VarName)); |
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[871] | 343 | if ismember(Param.ProjObject.ProjMode,{'inside','outside'}) |
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| 344 | if isfield(Data{1},VarName) |
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| 345 | MaxValue=max(DataOut.(VarName));% current max of histogram absissa |
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| 346 | MinValue=min(DataOut.(VarName));% current min of histogram absissa |
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| 347 | % VarMesh=Field.VarAttribute{ivar}.Mesh; |
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| 348 | MaxIndex=round(MaxValue/VarMesh); |
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| 349 | MinIndex=round(MinValue/VarMesh); |
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| 350 | MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field |
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| 351 | MinIndex_new=round(min(Field.(VarName)/VarMesh)); |
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| 352 | if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one |
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| 353 | DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values |
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| 354 | DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_new-MaxIndex)]; % append the new histo values |
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| 355 | end |
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| 356 | if MinIndex_new <= MinIndex-1 |
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| 357 | DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values |
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| 358 | DataOut.([VarName 'Histo'])=[zeros(1,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values |
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| 359 | ind_start=1; |
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| 360 | else |
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| 361 | ind_start=MinIndex_new-MinIndex+1; |
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| 362 | end |
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| 363 | DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)=... |
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| 364 | DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']); |
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| 365 | end |
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| 366 | elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean) |
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[867] | 367 | disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid'],checkrun) |
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| 368 | return |
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| 369 | else |
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| 370 | if errorvar(ivar)==0 |
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| 371 | check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else |
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[598] | 372 | else |
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[867] | 373 | check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else |
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[27] | 374 | end |
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[867] | 375 | Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
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| 376 | DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum |
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| 377 | NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point |
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[255] | 378 | end |
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[447] | 379 | end |
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[598] | 380 | %%%%%%%%%%%% END MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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| 381 | else |
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[609] | 382 | disp(errormsg) |
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[255] | 383 | end |
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[598] | 384 | end |
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| 385 | %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% |
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[871] | 386 | if ~ismember(Param.ProjObject.ProjMode,{'inside','outside'}) |
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| 387 | for ivar=1:length(Field.ListVarName) |
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| 388 | VarName=Field.ListVarName{ivar}; |
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| 389 | DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean |
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| 390 | end |
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[598] | 391 | end |
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[867] | 392 | nbmissing=NbField-nbfiles; |
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[598] | 393 | if nbmissing~=0 |
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[871] | 394 | disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun) |
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[598] | 395 | end |
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| 396 | if isempty(time) % time is read from files |
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| 397 | if isfield(Field,'Time') |
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| 398 | time_end=Field.Time(1);%last time read |
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| 399 | if ~isempty(time_1) |
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| 400 | DataOut.Time=time_1; |
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| 401 | DataOut.Time_end=time_end; |
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| 402 | end |
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[27] | 403 | end |
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[598] | 404 | else % time from ImaDoc prevails if it exists |
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| 405 | DataOut.Time=time(1); |
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| 406 | DataOut.Time_end=time(end); |
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| 407 | end |
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| 408 | |
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[609] | 409 | %% writing the result file |
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| 410 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); |
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[871] | 411 | if strcmp(FileExtOut,'.png') %case of images |
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[598] | 412 | if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16)) |
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| 413 | DataOut.A=uint16(DataOut.A); |
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| 414 | imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images |
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| 415 | else |
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| 416 | DataOut.A=uint8(DataOut.A); |
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| 417 | imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images |
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[27] | 418 | end |
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[609] | 419 | disp([OutputFile ' written']); |
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[871] | 420 | else %case of netcdf file , determine global attributes |
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[598] | 421 | errormsg=struct2nc(OutputFile,DataOut); %save result file |
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| 422 | if isempty(errormsg) |
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[609] | 423 | disp([OutputFile ' written']); |
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[598] | 424 | else |
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[609] | 425 | disp(['error in writting result file: ' errormsg]) |
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[598] | 426 | end |
---|
| 427 | end % end averaging loop |
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[255] | 428 | |
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[451] | 429 | %% open the result file with uvmat (in RUN mode) |
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| 430 | if checkrun |
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| 431 | uvmat(OutputFile)% open the last result file with uvmat |
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[810] | 432 | end |
---|