[944] | 1 | %'merge_proj': concatene several fields from series, project on a polar grid |
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| 2 | %------------------------------------------------------------------------ |
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| 3 | % function ParamOut=merge_proj(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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[1107] | 42 | % Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[944] | 43 | % http://www.legi.grenoble-inp.fr |
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| 44 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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| 45 | % |
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| 46 | % This file is part of the toolbox UVMAT. |
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| 47 | % |
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| 48 | % UVMAT is free software; you can redistribute it and/or modify |
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| 49 | % it under the terms of the GNU General Public License as published |
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| 50 | % by the Free Software Foundation; either version 2 of the license, |
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| 51 | % or (at your option) any later version. |
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| 52 | % |
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| 53 | % UVMAT is distributed in the hope that it will be useful, |
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| 54 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 55 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 56 | % GNU General Public License (see LICENSE.txt) for more details. |
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| 57 | %======================================================================= |
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| 58 | |
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| 59 | function ParamOut=merge_proj_polar(Param) |
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| 60 | |
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| 61 | %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed |
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| 62 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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| 63 | ParamOut.AllowInputSort='on';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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| 64 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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| 65 | ParamOut.NbSlice='on'; %nbre of slices ('off' by default) |
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| 66 | ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 67 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 68 | ParamOut.FieldTransform = 'on';%can use a transform function |
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| 69 | ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) |
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| 70 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', |
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| 71 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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| 72 | ParamOut.OutputDirExt='.polar';%set the output dir extension |
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| 73 | ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice |
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| 74 | %check the input files |
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| 75 | ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
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| 76 | first_j=[]; |
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| 77 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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| 78 | PairString=''; |
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| 79 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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| 80 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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| 81 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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| 82 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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| 83 | if ~exist(FirstFileName,'file') |
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| 84 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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| 85 | end |
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| 86 | return |
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| 87 | end |
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| 88 | |
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| 89 | %%%% specific input parameters |
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| 90 | % calculate the positions on which to interpolate |
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| 91 | radius_ref=450;% radius of the mountain top |
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| 92 | radius_shifted=-130:2:130;% radius shifted by the radius of the origin at the topography summit |
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| 93 | radius=radius_ref+radius_shifted;%radius from centre of the tank |
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| 94 | azimuth_arclength=(-150:2:400);%azimuth in arc length at origin position |
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| 95 | azimuth=pi/2-azimuth_arclength/radius_ref;%azimuth in radian |
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| 96 | [Radius,Azimuth]=meshgrid(radius,azimuth); |
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| 97 | XI=Radius.*cos(Azimuth);% set of x axis of the points where interpolqtion needs to be done |
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| 98 | YI=Radius.*sin(Azimuth)-radius_ref;% set of y axis of the points where interpolqtion needs to be done |
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| 99 | FieldNames={'vec(U,V)';'curl(U,V)';'div(U,V)'}; |
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| 100 | HeadData.ListVarName= {'radius','azimuth'} ; |
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| 101 | HeadData.VarDimName={'radius','azimuth'}; |
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| 102 | HeadData.VarAttribute={'coord_y','coord_x'} ; |
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| 103 | HeadData.radius=radius_shifted; |
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| 104 | HeadData.azimuth=azimuth_arclength; |
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| 105 | thresh2=16; % square of the interpolation range |
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| 106 | |
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| 107 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 108 | ParamOut=[]; %default output |
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| 109 | RUNHandle=[]; |
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| 110 | WaitbarHandle=[]; |
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| 111 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 112 | checkrun=1; |
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| 113 | if ischar(Param) |
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| 114 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 115 | checkrun=0; |
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| 116 | else |
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| 117 | hseries=findobj(allchild(0),'Tag','series'); |
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| 118 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 119 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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| 120 | end |
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| 121 | |
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| 122 | %% root input file type |
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| 123 | RootPath=Param.InputTable(:,1); |
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| 124 | RootFile=Param.InputTable(:,3); |
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| 125 | SubDir=Param.InputTable(:,2); |
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| 126 | %NomType=Param.InputTable(:,4); |
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| 127 | FileExt=Param.InputTable(:,5); |
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| 128 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 129 | %%%%%%%%%%%% |
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| 130 | % The cell array filecell is the list of input file names, while |
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| 131 | % filecell{iview,fileindex}: |
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| 132 | % iview: line in the table corresponding to a given file series |
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| 133 | % fileindex: file index within the file series, |
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| 134 | % 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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| 135 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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| 136 | %%%%%%%%%%%% |
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| 137 | % NbSlice=1;%default |
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| 138 | % if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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| 139 | % NbSlice=Param.IndexRange.NbSlice; |
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| 140 | % end |
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| 141 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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| 142 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 143 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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| 144 | NbField=NbField_j*NbField_i; %total number of fields |
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| 145 | |
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| 146 | %% define the name for result file (with path=RootPath{1}) |
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| 147 | OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files |
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| 148 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1',i1_series{1}(1)); |
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| 149 | CheckOverwrite=1;%default |
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| 150 | if isfield(Param,'CheckOverwrite') |
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| 151 | CheckOverwrite=Param.CheckOverwrite; |
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| 152 | end |
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| 153 | if ~CheckOverwrite && exist(OutputFile,'file') |
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| 154 | disp(['existing output file ' OutputFile ' already exists, skip to next field']) |
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| 155 | return% skip iteration if the mode overwrite is desactivated and the result file already exists |
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| 156 | end |
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| 157 | |
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| 158 | if ~isfield(Param,'InputFields') |
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| 159 | Param.InputFields.FieldName=''; |
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| 160 | end |
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| 161 | |
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| 162 | %% prepare output file content |
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| 163 | |
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| 164 | |
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| 165 | |
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| 166 | %% determine the file type on each line from the first input file |
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[984] | 167 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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[944] | 168 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 169 | for iview=1:NbView |
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| 170 | if ~exist(filecell{iview,1}','file') |
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| 171 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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| 172 | return |
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| 173 | end |
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| 174 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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| 175 | FileType{iview}=FileInfo{iview}.FileType; |
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| 176 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 177 | if CheckImage{iview} |
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| 178 | ParamIn{iview}=MovieObject{iview}; |
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| 179 | else |
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| 180 | ParamIn{iview}=Param.InputFields; |
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| 181 | end |
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| 182 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 183 | if ~isempty(j1_series{iview}) |
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| 184 | frame_index{iview}=j1_series{iview}; |
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| 185 | else |
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| 186 | frame_index{iview}=i1_series{iview}; |
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| 187 | end |
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| 188 | end |
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| 189 | if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject') |
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| 190 | disp_uvmat('ERROR','projection on a common grid is needed to concatene images: use a Projection Object of type ''plane'' with ProjMode=''interp_lin''',checkrun) |
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| 191 | return |
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| 192 | end |
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| 193 | |
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| 194 | %% calibration data and timing: read the ImaDoc files |
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| 195 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 196 | if size(time,1)>1 |
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| 197 | diff_time=max(max(diff(time))); |
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| 198 | if diff_time>0 |
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| 199 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun) |
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| 200 | end |
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| 201 | end |
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| 202 | if ~isempty(errormsg) |
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| 203 | disp_uvmat('WARNING',errormsg,checkrun) |
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| 204 | end |
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| 205 | time=mean(time,1); %averaged time taken for the merged field |
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| 206 | |
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| 207 | %% height z |
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| 208 | % position of projection plane |
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| 209 | |
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| 210 | ProjObjectCoord=XmlData{1}.GeometryCalib.SliceCoord; |
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| 211 | CoordUnit=XmlData{1}.GeometryCalib.CoordUnit; |
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| 212 | for iview =2:numel(XmlData) |
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| 213 | if ~(isfield(XmlData{iview},'GeometryCalib')&& isequal(XmlData{iview}.GeometryCalib.SliceCoord,ProjObjectCoord))... |
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| 214 | disp('error: geometric calibration missing or inconsistent plane positions') |
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| 215 | return |
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| 216 | end |
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| 217 | end |
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| 218 | |
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| 219 | |
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| 220 | %% coordinate transform or other user defined transform |
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| 221 | transform_fct='';%default fct handle |
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| 222 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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| 223 | currentdir=pwd; |
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| 224 | cd(Param.FieldTransform.TransformPath) |
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| 225 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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| 226 | cd (currentdir) |
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| 227 | if isfield(Param,'TransformInput') |
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| 228 | for iview=1:NbView |
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| 229 | XmlData{iview}.TransformInput=Param.TransformInput; |
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| 230 | end |
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| 231 | end |
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| 232 | end |
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| 233 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 234 | % EDIT FROM HERE |
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| 235 | |
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| 236 | %% check the validity of input file types |
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| 237 | for iview=1:NbView |
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| 238 | if ~isequal(CheckNc{iview},1) |
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| 239 | disp_uvmat('ERROR','input files needs to be in netcdf (extension .nc)',checkrun) |
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| 240 | return |
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| 241 | end |
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| 242 | end |
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| 243 | |
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| 244 | % %% output file type |
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| 245 | if isempty(j1_series{1}) |
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| 246 | NomTypeOut='_1'; |
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| 247 | else |
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| 248 | NomTypeOut='_1_1'; |
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| 249 | end |
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| 250 | RootFileOut=RootFile{1}; |
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| 251 | for iview=2:NbView |
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| 252 | if ~strcmp(RootFile{iview},RootFile{1}) |
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| 253 | RootFileOut='mproj'; |
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| 254 | break |
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| 255 | end |
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| 256 | end |
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| 257 | |
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| 258 | |
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| 259 | %% MAIN LOOP ON FIELDS |
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| 260 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 261 | % for i_slice=1:NbSlice |
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| 262 | % index_slice=i_slice:NbSlice:NbField;% select file indices of the slice |
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| 263 | % NbFiles=0; |
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| 264 | % nbmissing=0; |
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| 265 | |
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| 266 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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| 267 | tstart=tic; %used to record the computing time |
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| 268 | TimeData=[]; |
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| 269 | |
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| 270 | for index=1:NbField |
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| 271 | disp(['index=' num2str(index)]) |
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[1082] | 272 | %disp(['ellapsed time ' num2str(toc(tstart)/60,4) ' minutes']) |
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[944] | 273 | update_waitbar(WaitbarHandle,index/NbField) |
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| 274 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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| 275 | disp('program stopped by user') |
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| 276 | return |
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| 277 | end |
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| 278 | |
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| 279 | %% generating the name of the merged field |
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| 280 | i1=i1_series{1}(index); |
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| 281 | if ~isempty(i2_series{end}) |
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| 282 | i2=i2_series{end}(index); |
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| 283 | else |
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| 284 | i2=i1; |
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| 285 | end |
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| 286 | j1=1; |
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| 287 | j2=1; |
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| 288 | if ~isempty(j1_series{1}) |
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| 289 | j1=j1_series{1}(index); |
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| 290 | if ~isempty(j2_series{end}) |
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| 291 | j2=j2_series{end}(index); |
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| 292 | else |
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| 293 | j2=j1; |
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| 294 | end |
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| 295 | end |
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| 296 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,'.nc',NomTypeOut,i1,i2,j1,j2); |
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| 297 | |
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| 298 | |
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| 299 | %% z position |
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| 300 | ZIndex=mod(i1_series{1}(index)-1,NbSlice_calib{1})+1;%Zindex for phys transform |
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| 301 | ZPosNew=ProjObjectCoord(ZIndex,3); |
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| 302 | if index==1 |
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| 303 | ZPos=ZPosNew; |
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| 304 | else |
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| 305 | if ZPosNew~=ZPos |
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| 306 | disp('inconsistent z positions in the series') |
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| 307 | return |
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| 308 | end |
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| 309 | end |
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| 310 | % radius of the topography section at z position |
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| 311 | ind_mask=[]; |
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| 312 | if ZPos<20 |
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| 313 | TopoRadius=40*sin(acos((20+ZPos)/40)); |
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| 314 | ind_mask=(XI'.*XI'+YI'.*YI')<TopoRadius*TopoRadius;% indidces of data to mask |
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| 315 | end |
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| 316 | if ~CheckOverwrite && exist(OutputFile,'file') |
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| 317 | disp(['existing output file ' OutputFile ' already exists, skip to next field']) |
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| 318 | continue% skip iteration if the mode overwrite is desactivated and the result file already exists |
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| 319 | end |
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| 320 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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| 321 | Data=cell(1,NbView);%initiate the set Data |
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| 322 | timeread=zeros(1,NbView); |
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| 323 | for iview=1:NbView |
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| 324 | %% reading input file(s) |
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| 325 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index)); |
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| 326 | if ~isempty(errormsg) |
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| 327 | disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun) |
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| 328 | return |
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| 329 | end |
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| 330 | ListVar=Data{iview}.ListVarName; |
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| 331 | for ilist=1:numel(ListVar) |
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| 332 | Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations |
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| 333 | end |
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| 334 | % get the time defined in the current file if not already defined from the xml file |
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| 335 | if ~isempty(time) && isfield(Data{iview},'Time') |
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| 336 | timeread(iview)=Data{iview}.Time; |
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| 337 | end |
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| 338 | if ~isempty(NbSlice_calib) |
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| 339 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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| 340 | end |
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| 341 | |
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| 342 | %% transform the input field (e.g; phys) if requested (no transform involving two input fields) |
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| 343 | if ~isempty(transform_fct) |
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| 344 | if nargin(transform_fct)>=2 |
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| 345 | Data{iview}=transform_fct(Data{iview},XmlData{iview}); |
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| 346 | else |
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| 347 | Data{iview}=transform_fct(Data{iview}); |
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| 348 | end |
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| 349 | end |
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| 350 | |
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| 351 | %% calculate tps coefficients |
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| 352 | Data{iview}=tps_coeff_field(Data{iview},1); |
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| 353 | |
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| 354 | %% projection on the polar grid |
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| 355 | [DataOut,VarAttribute,errormsg]=calc_field_tps(Data{iview}.Coord_tps,Data{iview}.NbCentre,Data{iview}.SubRange,... |
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| 356 | cat(3,Data{iview}.U_tps,Data{iview}.V_tps),FieldNames,cat(3,XI,YI)); |
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| 357 | % set to NaN interpolation points which are too far from any initial data (more than 2 CoordMesh) |
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| 358 | Coord=permute(Data{iview}.Coord_tps,[1 3 2]); |
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| 359 | Coord=reshape(Coord,size(Coord,1)*size(Coord,2),2); |
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| 360 | if exist('scatteredInterpolant','file')%recent Matlab versions |
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| 361 | F=scatteredInterpolant(Coord,Coord(:,1),'nearest'); |
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| 362 | G=scatteredInterpolant(Coord,Coord(:,2),'nearest'); |
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| 363 | else |
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| 364 | F=TriScatteredInterp(Coord,Coord(:,1),'nearest'); |
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| 365 | G=TriScatteredInterp(Coord,Coord(:,2),'nearest'); |
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| 366 | end |
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| 367 | Distx=F(XI,YI)-XI;% diff of x coordinates with the nearest measurement point |
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| 368 | Disty=G(XI,YI)-YI;% diff of y coordinates with the nearest measurement point |
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| 369 | Dist=Distx.*Distx+Disty.*Disty; |
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| 370 | ListVarName=(fieldnames(DataOut))'; |
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| 371 | VarDimName=cell(size(ListVarName)); |
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| 372 | ProjData{iview}=HeadData; |
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| 373 | ProjData{iview}.ListVarName= [ProjData{iview}.ListVarName ListVarName]; |
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| 374 | ProjData{iview}.VarDimName={'radius','azimuth'}; |
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| 375 | ProjData{iview}.VarAttribute=[{'coord_x'} {'coord_y'} VarAttribute]; |
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[1082] | 376 | % for ivar=1:numel(ListVarName) |
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| 377 | % ProjData{iview}.VarDimName{ivar+2}={'radius','azimuth'}; |
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| 378 | % VarName=ListVarName{ivar}; |
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| 379 | % if ~isempty(thresh2) |
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| 380 | % DataOut.(VarName)(Dist>thresh2)=NaN;% put to NaN interpolated positions further than RangeInterp from initial data |
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| 381 | % end |
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| 382 | % ProjData{iview}.(VarName)=(DataOut.(VarName))'; |
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| 383 | % end |
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[944] | 384 | |
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| 385 | end |
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| 386 | %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%% |
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| 387 | |
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| 388 | %% merge the NbView fields |
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| 389 | [MergeData,errormsg]=merge_field(ProjData); |
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| 390 | if ~isempty(errormsg) |
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| 391 | disp_uvmat('ERROR',errormsg,checkrun); |
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| 392 | return |
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| 393 | end |
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| 394 | |
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| 395 | |
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| 396 | %% time of the merged field: take the average of the different views |
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| 397 | if ~isempty(time) |
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| 398 | timeread=time(index); |
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| 399 | elseif ~isempty(find(timeread))% time defined from ImaDoc |
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| 400 | timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined) |
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| 401 | else |
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| 402 | timeread=index;% take time=file index |
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| 403 | end |
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| 404 | |
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| 405 | %% rotating the velocity vectors to the local axis of the polatr coordinates |
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| 406 | Unew=MergeData.U.*sin(Azimuth')-MergeData.V.*cos(Azimuth'); |
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| 407 | Vnew=MergeData.U.*cos(Azimuth')+MergeData.V.*sin(Azimuth'); |
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| 408 | if ~isempty(ind_mask) |
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| 409 | Unew(ind_mask)=NaN; |
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| 410 | Vnew(ind_mask)=NaN; |
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| 411 | MergeData.curl(ind_mask)=NaN; |
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| 412 | MergeData.div(ind_mask)=NaN; |
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| 413 | end |
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| 414 | [npy,npx]=size(Unew); |
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| 415 | |
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| 416 | %% create the output file for the first iteration of the loop |
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| 417 | if isempty(TimeData)% initialize |
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| 418 | TimeData.ListGlobalAttribute={'Conventions','Project','CoordUnit','TimeUnit','ZPos','Time'}; |
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| 419 | TimeData.Conventions='uvmat'; |
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| 420 | TimeData.Project='2016_Circumpolar'; |
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| 421 | TimeData.CoordUnit='cm'; |
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| 422 | TimeData.TimeUnit='s'; |
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| 423 | TimeData.ZPos=ZPos; |
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| 424 | TimeData.ListVarName={'radius','azimuth','U','V','curl','div'}; |
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| 425 | TimeData.VarDimName={'radius','azimuth',{'radius','azimuth'},{'radius','azimuth'}... |
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| 426 | {'radius','azimuth'},{'radius','azimuth'}}; |
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| 427 | TimeData.VarAttribute{1}.Role=''; |
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| 428 | TimeData.VarAttribute{2}.Role=''; |
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| 429 | TimeData.VarAttribute{3}.Role='vector_x'; |
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| 430 | TimeData.VarAttribute{4}.Role='vector_y'; |
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| 431 | TimeData.VarAttribute{5}.Role='scalar'; |
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| 432 | TimeData.VarAttribute{6}.Role='scalar'; |
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| 433 | |
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| 434 | TimeData.radius=radius_shifted; |
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| 435 | TimeData.azimuth=azimuth_arclength; |
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| 436 | end |
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| 437 | |
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| 438 | %% append data to the netcdf file for next iterations |
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| 439 | TimeData.Time=timeread; |
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| 440 | TimeData.U=Unew; |
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| 441 | TimeData.V=Vnew; |
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| 442 | TimeData.curl=MergeData.curl; |
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| 443 | TimeData.div=MergeData.div; |
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| 444 | |
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| 445 | error=struct2nc(OutputFile,TimeData);%save result file |
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| 446 | if isempty(error) |
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| 447 | disp(['output file ' OutputFile ' written']) |
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| 448 | else |
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| 449 | disp(error) |
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| 450 | end |
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| 451 | ellapsed_time=toc(tstart); |
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| 452 | disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes']) |
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| 453 | end |
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| 454 | |
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| 455 | ellapsed_time=toc(tstart); |
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| 456 | disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes']) |
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| 457 | disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration']) |
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| 458 | |
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| 459 | %'merge_field': concatene fields |
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| 460 | %------------------------------------------------------------------------ |
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| 461 | function [MergeData,errormsg]=merge_field(Data) |
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| 462 | %% default output |
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| 463 | if isempty(Data)||~iscell(Data) |
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| 464 | MergeData=[]; |
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| 465 | return |
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| 466 | end |
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| 467 | errormsg=''; |
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| 468 | MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field |
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| 469 | NbView=length(Data); |
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| 470 | if NbView==1% if there is only one field, just reproduce it in MergeData |
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| 471 | return |
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| 472 | end |
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| 473 | |
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| 474 | %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
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| 475 | [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); |
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| 476 | if ~isempty(errormsg) |
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| 477 | return |
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| 478 | end |
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| 479 | |
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| 480 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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| 481 | for icell=1:length(CellInfo) |
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| 482 | if NbDim(icell)~=1 % skip field cells which are of dim 1 |
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| 483 | switch CellInfo{icell}.CoordType |
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| 484 | case 'scattered' %case of input fields with unstructured coordinates: just concatene data |
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| 485 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
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| 486 | VarName=Data{1}.ListVarName{ivar}; |
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| 487 | for iview=2:NbView |
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| 488 | MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
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| 489 | end |
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| 490 | end |
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| 491 | case 'grid' %case of fields defined on a structured grid |
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| 492 | FFName=''; |
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| 493 | if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) |
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| 494 | FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable |
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| 495 | MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) |
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| 496 | MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; |
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| 497 | MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; |
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| 498 | end |
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| 499 | % select good data on each view |
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| 500 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
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| 501 | VarName=Data{1}.ListVarName{ivar}; |
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| 502 | for iview=1:NbView |
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| 503 | if isempty(FFName) |
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| 504 | check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else |
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| 505 | else |
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| 506 | check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else |
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| 507 | end |
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| 508 | Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
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| 509 | if iview==1 |
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| 510 | %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field |
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| 511 | MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
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| 512 | NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point |
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| 513 | elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) |
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| 514 | errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; |
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| 515 | return |
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| 516 | else |
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| 517 | MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data |
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| 518 | NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else |
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| 519 | end |
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| 520 | end |
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| 521 | MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point |
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| 522 | MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data |
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| 523 | end |
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| 524 | end |
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| 525 | % if isempty(FFName) |
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| 526 | % FFName='FF'; |
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| 527 | % end |
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| 528 | % MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data |
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| 529 | % MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data |
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| 530 | end |
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| 531 | end |
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| 532 | |
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| 533 | |
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| 534 | |
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