[943] | 1 | %'merge_proj': concatene several fields from series, project on a polar grid |
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[938] | 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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[1071] | 42 | % Copyright 2008-2020, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[938] | 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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[939] | 63 | ParamOut.AllowInputSort='on';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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[938] | 64 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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[1068] | 65 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default) |
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[938] | 66 | ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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[940] | 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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[938] | 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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[939] | 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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[938] | 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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[939] | 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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[940] | 92 | radius_shifted=-130:2:130;% radius shifted by the radius of the origin at the topography summit |
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[939] | 93 | radius=radius_ref+radius_shifted;%radius from centre of the tank |
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[940] | 94 | azimuth_arclength=(-150:2:400);%azimuth in arc length at origin position |
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[939] | 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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[1058] | 102 | HeadData.VarAttribute{1}.Role='coord_y'; |
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| 103 | HeadData.VarAttribute{2}.Role='coord_x'; |
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[939] | 104 | HeadData.radius=radius_shifted; |
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| 105 | HeadData.azimuth=azimuth_arclength; |
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[940] | 106 | thresh2=16; % square of the interpolation range |
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[943] | 107 | |
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[938] | 108 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 109 | ParamOut=[]; %default output |
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| 110 | RUNHandle=[]; |
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| 111 | WaitbarHandle=[]; |
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| 112 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 113 | checkrun=1; |
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| 114 | if ischar(Param) |
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| 115 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 116 | checkrun=0; |
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| 117 | else |
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| 118 | hseries=findobj(allchild(0),'Tag','series'); |
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| 119 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 120 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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| 121 | end |
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| 122 | |
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| 123 | %% root input file type |
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| 124 | RootPath=Param.InputTable(:,1); |
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| 125 | RootFile=Param.InputTable(:,3); |
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| 126 | SubDir=Param.InputTable(:,2); |
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[939] | 127 | %NomType=Param.InputTable(:,4); |
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[938] | 128 | FileExt=Param.InputTable(:,5); |
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| 129 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 130 | %%%%%%%%%%%% |
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| 131 | % The cell array filecell is the list of input file names, while |
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| 132 | % filecell{iview,fileindex}: |
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| 133 | % iview: line in the table corresponding to a given file series |
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| 134 | % fileindex: file index within the file series, |
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| 135 | % 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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| 136 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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| 137 | %%%%%%%%%%%% |
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| 138 | % NbSlice=1;%default |
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| 139 | % if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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| 140 | % NbSlice=Param.IndexRange.NbSlice; |
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| 141 | % end |
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| 142 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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| 143 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 144 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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| 145 | NbField=NbField_j*NbField_i; %total number of fields |
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| 146 | |
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[940] | 147 | %% define the name for result file (with path=RootPath{1}) |
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| 148 | OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files |
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[944] | 149 | % OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1',i1_series{1}(1)); |
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| 150 | % CheckOverwrite=1;%default |
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| 151 | % if isfield(Param,'CheckOverwrite') |
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| 152 | % CheckOverwrite=Param.CheckOverwrite; |
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| 153 | % end |
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| 154 | % if ~CheckOverwrite && exist(OutputFile,'file') |
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| 155 | % disp(['existing output file ' OutputFile ' already exists, skip to next field']) |
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| 156 | % return% skip iteration if the mode overwrite is desactivated and the result file already exists |
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| 157 | % end |
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[940] | 158 | |
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| 159 | if ~isfield(Param,'InputFields') |
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| 160 | Param.InputFields.FieldName=''; |
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| 161 | end |
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| 162 | |
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| 163 | |
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[938] | 164 | %% determine the file type on each line from the first input file |
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[984] | 165 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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[938] | 166 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 167 | for iview=1:NbView |
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| 168 | if ~exist(filecell{iview,1}','file') |
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| 169 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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| 170 | return |
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| 171 | end |
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| 172 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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| 173 | FileType{iview}=FileInfo{iview}.FileType; |
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| 174 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 175 | if CheckImage{iview} |
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| 176 | ParamIn{iview}=MovieObject{iview}; |
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| 177 | else |
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| 178 | ParamIn{iview}=Param.InputFields; |
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| 179 | end |
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| 180 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 181 | if ~isempty(j1_series{iview}) |
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| 182 | frame_index{iview}=j1_series{iview}; |
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| 183 | else |
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| 184 | frame_index{iview}=i1_series{iview}; |
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| 185 | end |
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| 186 | end |
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| 187 | if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject') |
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| 188 | 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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| 189 | return |
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| 190 | end |
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| 191 | |
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| 192 | %% calibration data and timing: read the ImaDoc files |
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| 193 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 194 | if size(time,1)>1 |
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| 195 | diff_time=max(max(diff(time))); |
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| 196 | if diff_time>0 |
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| 197 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun) |
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| 198 | end |
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| 199 | end |
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| 200 | if ~isempty(errormsg) |
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| 201 | disp_uvmat('WARNING',errormsg,checkrun) |
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| 202 | end |
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| 203 | time=mean(time,1); %averaged time taken for the merged field |
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| 204 | |
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[939] | 205 | %% height z |
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| 206 | % position of projection plane |
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| 207 | |
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| 208 | ProjObjectCoord=XmlData{1}.GeometryCalib.SliceCoord; |
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| 209 | CoordUnit=XmlData{1}.GeometryCalib.CoordUnit; |
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| 210 | for iview =2:numel(XmlData) |
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| 211 | if ~(isfield(XmlData{iview},'GeometryCalib')&& isequal(XmlData{iview}.GeometryCalib.SliceCoord,ProjObjectCoord))... |
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[943] | 212 | disp('error: geometric calibration missing or inconsistent plane positions') |
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[939] | 213 | return |
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| 214 | end |
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| 215 | end |
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| 216 | |
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| 217 | |
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[938] | 218 | %% coordinate transform or other user defined transform |
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| 219 | transform_fct='';%default fct handle |
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| 220 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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| 221 | currentdir=pwd; |
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| 222 | cd(Param.FieldTransform.TransformPath) |
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| 223 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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| 224 | cd (currentdir) |
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| 225 | if isfield(Param,'TransformInput') |
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| 226 | for iview=1:NbView |
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| 227 | XmlData{iview}.TransformInput=Param.TransformInput; |
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| 228 | end |
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| 229 | end |
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| 230 | end |
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| 231 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 232 | % EDIT FROM HERE |
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| 233 | |
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| 234 | %% check the validity of input file types |
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| 235 | for iview=1:NbView |
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[939] | 236 | if ~isequal(CheckNc{iview},1) |
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| 237 | disp_uvmat('ERROR','input files needs to be in netcdf (extension .nc)',checkrun) |
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[938] | 238 | return |
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| 239 | end |
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| 240 | end |
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| 241 | |
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[940] | 242 | % %% output file type |
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[943] | 243 | if isempty(j1_series{1}) |
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| 244 | NomTypeOut='_1'; |
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| 245 | else |
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| 246 | NomTypeOut='_1_1'; |
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| 247 | end |
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| 248 | RootFileOut=RootFile{1}; |
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| 249 | for iview=2:NbView |
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| 250 | if ~strcmp(RootFile{iview},RootFile{1}) |
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| 251 | RootFileOut='mproj'; |
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| 252 | break |
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| 253 | end |
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| 254 | end |
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[938] | 255 | |
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| 256 | |
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| 257 | %% MAIN LOOP ON FIELDS |
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| 258 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 259 | % for i_slice=1:NbSlice |
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| 260 | % index_slice=i_slice:NbSlice:NbField;% select file indices of the slice |
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| 261 | % NbFiles=0; |
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| 262 | % nbmissing=0; |
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| 263 | |
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[939] | 264 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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[938] | 265 | tstart=tic; %used to record the computing time |
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[944] | 266 | CheckOverwrite=1;%default |
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| 267 | if isfield(Param,'CheckOverwrite') |
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| 268 | CheckOverwrite=Param.CheckOverwrite; |
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| 269 | end |
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[1068] | 270 | NbField |
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[938] | 271 | for index=1:NbField |
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[939] | 272 | update_waitbar(WaitbarHandle,index/NbField) |
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[938] | 273 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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| 274 | disp('program stopped by user') |
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| 275 | return |
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| 276 | end |
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| 277 | |
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[943] | 278 | %% generating the name of the merged field |
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| 279 | i1=i1_series{1}(index); |
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| 280 | if ~isempty(i2_series{end}) |
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| 281 | i2=i2_series{end}(index); |
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| 282 | else |
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| 283 | i2=i1; |
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| 284 | end |
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| 285 | j1=1; |
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| 286 | j2=1; |
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| 287 | if ~isempty(j1_series{1}) |
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| 288 | j1=j1_series{1}(index); |
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| 289 | if ~isempty(j2_series{end}) |
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| 290 | j2=j2_series{end}(index); |
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| 291 | else |
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| 292 | j2=j1; |
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| 293 | end |
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| 294 | end |
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| 295 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,'.nc',NomTypeOut,i1,i2,j1,j2); |
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| 296 | if ~CheckOverwrite && exist(OutputFile,'file') |
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| 297 | disp(['existing output file ' OutputFile ' already exists, skip to next field']) |
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| 298 | continue% skip iteration if the mode overwrite is desactivated and the result file already exists |
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| 299 | end |
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| 300 | |
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[940] | 301 | %% z position |
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| 302 | ZIndex=mod(i1_series{1}(index)-1,NbSlice_calib{1})+1;%Zindex for phys transform |
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[943] | 303 | ZPosNew=ProjObjectCoord(ZIndex,3); |
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[940] | 304 | if index==1 |
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[943] | 305 | ZPos=ZPosNew; |
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[938] | 306 | else |
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[943] | 307 | if ZPosNew~=ZPos |
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[940] | 308 | disp('inconsistent z positions in the series') |
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| 309 | return |
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[938] | 310 | end |
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| 311 | end |
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[943] | 312 | % radius of the topography section at z position |
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[940] | 313 | ind_mask=[]; |
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| 314 | if ZPos<20 |
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| 315 | TopoRadius=40*sin(acos((20+ZPos)/40)); |
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| 316 | ind_mask=(XI'.*XI'+YI'.*YI')<TopoRadius*TopoRadius;% indidces of data to mask |
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[938] | 317 | end |
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[939] | 318 | |
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[938] | 319 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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| 320 | Data=cell(1,NbView);%initiate the set Data |
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| 321 | timeread=zeros(1,NbView); |
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| 322 | for iview=1:NbView |
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[939] | 323 | %% reading input file(s) |
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[938] | 324 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index)); |
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| 325 | if ~isempty(errormsg) |
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| 326 | disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun) |
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| 327 | return |
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| 328 | end |
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| 329 | ListVar=Data{iview}.ListVarName; |
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| 330 | for ilist=1:numel(ListVar) |
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| 331 | Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations |
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| 332 | end |
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| 333 | % get the time defined in the current file if not already defined from the xml file |
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| 334 | if ~isempty(time) && isfield(Data{iview},'Time') |
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| 335 | timeread(iview)=Data{iview}.Time; |
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| 336 | end |
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| 337 | if ~isempty(NbSlice_calib) |
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| 338 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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| 339 | end |
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| 340 | |
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| 341 | %% transform the input field (e.g; phys) if requested (no transform involving two input fields) |
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| 342 | if ~isempty(transform_fct) |
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| 343 | if nargin(transform_fct)>=2 |
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| 344 | Data{iview}=transform_fct(Data{iview},XmlData{iview}); |
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| 345 | else |
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| 346 | Data{iview}=transform_fct(Data{iview}); |
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| 347 | end |
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| 348 | end |
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| 349 | |
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[939] | 350 | %% calculate tps coefficients |
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| 351 | Data{iview}=tps_coeff_field(Data{iview},1); |
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[1068] | 352 | 'tps_coeff done' |
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[939] | 353 | %% projection on the polar grid |
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| 354 | [DataOut,VarAttribute,errormsg]=calc_field_tps(Data{iview}.Coord_tps,Data{iview}.NbCentre,Data{iview}.SubRange,... |
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| 355 | cat(3,Data{iview}.U_tps,Data{iview}.V_tps),FieldNames,cat(3,XI,YI)); |
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[1068] | 356 | if ~isempty(errormsg) |
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| 357 | disp(errormsg) |
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| 358 | end |
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| 359 | |
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[940] | 360 | % set to NaN interpolation points which are too far from any initial data (more than 2 CoordMesh) |
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| 361 | Coord=permute(Data{iview}.Coord_tps,[1 3 2]); |
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| 362 | Coord=reshape(Coord,size(Coord,1)*size(Coord,2),2); |
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| 363 | if exist('scatteredInterpolant','file')%recent Matlab versions |
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| 364 | F=scatteredInterpolant(Coord,Coord(:,1),'nearest'); |
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| 365 | G=scatteredInterpolant(Coord,Coord(:,2),'nearest'); |
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| 366 | else |
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| 367 | F=TriScatteredInterp(Coord,Coord(:,1),'nearest'); |
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| 368 | G=TriScatteredInterp(Coord,Coord(:,2),'nearest'); |
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| 369 | end |
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[1068] | 370 | 'Interp done' |
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[940] | 371 | Distx=F(XI,YI)-XI;% diff of x coordinates with the nearest measurement point |
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| 372 | Disty=G(XI,YI)-YI;% diff of y coordinates with the nearest measurement point |
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| 373 | Dist=Distx.*Distx+Disty.*Disty; |
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[939] | 374 | ListVarName=(fieldnames(DataOut))'; |
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[940] | 375 | VarDimName=cell(size(ListVarName)); |
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[939] | 376 | ProjData{iview}=HeadData; |
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| 377 | ProjData{iview}.ListVarName= [ProjData{iview}.ListVarName ListVarName]; |
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| 378 | ProjData{iview}.VarDimName={'radius','azimuth'}; |
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[1058] | 379 | % ProjData{iview}.VarAttribute{1}.Role='coord_y'; |
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| 380 | % ProjData{iview}.VarAttribute{2}.Role='coord_x'; |
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| 381 | ProjData{iview}.VarAttribute=[ProjData{iview}.VarAttribute VarAttribute]; |
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[939] | 382 | for ivar=1:numel(ListVarName) |
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| 383 | ProjData{iview}.VarDimName{ivar+2}={'radius','azimuth'}; |
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[940] | 384 | VarName=ListVarName{ivar}; |
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| 385 | if ~isempty(thresh2) |
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| 386 | DataOut.(VarName)(Dist>thresh2)=NaN;% put to NaN interpolated positions further than RangeInterp from initial data |
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| 387 | end |
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| 388 | ProjData{iview}.(VarName)=(DataOut.(VarName))'; |
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[938] | 389 | end |
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[940] | 390 | |
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[938] | 391 | end |
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| 392 | %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%% |
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[939] | 393 | |
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[938] | 394 | %% merge the NbView fields |
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[1068] | 395 | ProjData |
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[939] | 396 | [MergeData,errormsg]=merge_field(ProjData); |
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[938] | 397 | if ~isempty(errormsg) |
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| 398 | disp_uvmat('ERROR',errormsg,checkrun); |
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| 399 | return |
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| 400 | end |
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[939] | 401 | |
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[943] | 402 | |
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[938] | 403 | %% time of the merged field: take the average of the different views |
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| 404 | if ~isempty(time) |
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[939] | 405 | timeread=time(index); |
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[938] | 406 | elseif ~isempty(find(timeread))% time defined from ImaDoc |
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| 407 | timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined) |
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| 408 | else |
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[939] | 409 | timeread=index;% take time=file index |
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[938] | 410 | end |
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[939] | 411 | |
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| 412 | %% rotating the velocity vectors to the local axis of the polatr coordinates |
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| 413 | Unew=MergeData.U.*sin(Azimuth')-MergeData.V.*cos(Azimuth'); |
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[940] | 414 | Vnew=MergeData.U.*cos(Azimuth')+MergeData.V.*sin(Azimuth'); |
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[939] | 415 | if ~isempty(ind_mask) |
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[940] | 416 | Unew(ind_mask)=NaN; |
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| 417 | Vnew(ind_mask)=NaN; |
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[939] | 418 | MergeData.curl(ind_mask)=NaN; |
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| 419 | MergeData.div(ind_mask)=NaN; |
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[940] | 420 | end |
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[943] | 421 | [npy,npx]=size(Unew); |
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[939] | 422 | |
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[943] | 423 | %% create the output file for the first iteration of the loop |
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| 424 | if index==1 |
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| 425 | TimeData.ListGlobalAttribute={'Conventions','Project','CoordUnit','TimeUnit','ZPos','Time'}; |
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| 426 | TimeData.Conventions='uvmat'; |
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| 427 | TimeData.Project='2016_Circumpolar'; |
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| 428 | TimeData.CoordUnit='cm'; |
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| 429 | TimeData.TimeUnit='s'; |
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| 430 | TimeData.ZPos=ZPos; |
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| 431 | TimeData.ListVarName={'radius','azimuth','U','V','curl','div'}; |
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| 432 | TimeData.VarDimName={'radius','azimuth',{'radius','azimuth'},{'radius','azimuth'}... |
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| 433 | {'radius','azimuth'},{'radius','azimuth'}}; |
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| 434 | TimeData.VarAttribute{1}.Role=''; |
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| 435 | TimeData.VarAttribute{2}.Role=''; |
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| 436 | TimeData.VarAttribute{3}.Role='vector_x'; |
---|
| 437 | TimeData.VarAttribute{4}.Role='vector_y'; |
---|
| 438 | TimeData.VarAttribute{5}.Role='scalar'; |
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| 439 | TimeData.VarAttribute{6}.Role='scalar'; |
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| 440 | |
---|
| 441 | TimeData.radius=radius_shifted; |
---|
| 442 | TimeData.azimuth=azimuth_arclength; |
---|
| 443 | end |
---|
| 444 | |
---|
| 445 | %% append data to the netcdf file for next iterations |
---|
| 446 | TimeData.Time=timeread; |
---|
| 447 | TimeData.U=Unew; |
---|
| 448 | TimeData.V=Vnew; |
---|
| 449 | TimeData.curl=MergeData.curl; |
---|
| 450 | TimeData.div=MergeData.div; |
---|
[939] | 451 | |
---|
[1068] | 452 | error=struct2nc(OutputFile,TimeData);%save result file |
---|
[943] | 453 | if isempty(error) |
---|
| 454 | disp(['output file ' OutputFile ' written']) |
---|
| 455 | else |
---|
| 456 | disp(error) |
---|
| 457 | end |
---|
| 458 | ellapsed_time=toc(tstart); |
---|
[1068] | 459 | disp(['ellapsed time since start ' num2str(ellapsed_time/60,2) ' minutes']) |
---|
[940] | 460 | end |
---|
[943] | 461 | |
---|
[938] | 462 | disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration']) |
---|
| 463 | |
---|
[1058] | 464 | % %'merge_field': concatene fields |
---|
| 465 | % %------------------------------------------------------------------------ |
---|
| 466 | % function [MergeData,errormsg]=merge_field(Data) |
---|
| 467 | % %% default output |
---|
| 468 | % if isempty(Data)||~iscell(Data) |
---|
| 469 | % MergeData=[]; |
---|
| 470 | % return |
---|
| 471 | % end |
---|
| 472 | % errormsg=''; |
---|
| 473 | % MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field |
---|
| 474 | % NbView=length(Data); |
---|
| 475 | % if NbView==1% if there is only one field, just reproduce it in MergeData |
---|
| 476 | % return |
---|
| 477 | % end |
---|
| 478 | % |
---|
| 479 | % %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
---|
| 480 | % [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); |
---|
| 481 | % if ~isempty(errormsg) |
---|
| 482 | % return |
---|
| 483 | % end |
---|
| 484 | % |
---|
| 485 | % %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
---|
| 486 | % for icell=1:length(CellInfo) |
---|
| 487 | % if NbDim(icell)~=1 % skip field cells which are of dim 1 |
---|
| 488 | % switch CellInfo{icell}.CoordType |
---|
| 489 | % case 'scattered' %case of input fields with unstructured coordinates: just concatene data |
---|
| 490 | % for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
---|
| 491 | % VarName=Data{1}.ListVarName{ivar}; |
---|
| 492 | % for iview=2:NbView |
---|
| 493 | % MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
---|
| 494 | % end |
---|
| 495 | % end |
---|
| 496 | % case 'grid' %case of fields defined on a structured grid |
---|
| 497 | % FFName=''; |
---|
| 498 | % if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) |
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| 499 | % FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable |
---|
| 500 | % MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) |
---|
| 501 | % MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; |
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| 502 | % MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; |
---|
| 503 | % end |
---|
| 504 | % % select good data on each view |
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| 505 | % for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
---|
| 506 | % VarName=Data{1}.ListVarName{ivar}; |
---|
| 507 | % for iview=1:NbView |
---|
| 508 | % if isempty(FFName) |
---|
| 509 | % check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else |
---|
| 510 | % else |
---|
| 511 | % check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else |
---|
| 512 | % end |
---|
| 513 | % Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
---|
| 514 | % if iview==1 |
---|
| 515 | % %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field |
---|
| 516 | % MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
---|
| 517 | % NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point |
---|
| 518 | % elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) |
---|
| 519 | % errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; |
---|
| 520 | % return |
---|
| 521 | % else |
---|
| 522 | % MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data |
---|
| 523 | % NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else |
---|
| 524 | % end |
---|
| 525 | % end |
---|
| 526 | % MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point |
---|
| 527 | % MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data |
---|
| 528 | % end |
---|
| 529 | % end |
---|
| 530 | % |
---|
| 531 | % end |
---|
| 532 | % end |
---|
| 533 | |
---|
| 534 | |
---|
[938] | 535 | %'merge_field': concatene fields |
---|
| 536 | %------------------------------------------------------------------------ |
---|
| 537 | function [MergeData,errormsg]=merge_field(Data) |
---|
| 538 | %% default output |
---|
| 539 | if isempty(Data)||~iscell(Data) |
---|
| 540 | MergeData=[]; |
---|
| 541 | return |
---|
| 542 | end |
---|
| 543 | errormsg=''; |
---|
| 544 | MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field |
---|
| 545 | NbView=length(Data); |
---|
| 546 | if NbView==1% if there is only one field, just reproduce it in MergeData |
---|
[1058] | 547 | return |
---|
[938] | 548 | end |
---|
| 549 | |
---|
| 550 | %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
---|
| 551 | [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); |
---|
| 552 | if ~isempty(errormsg) |
---|
| 553 | return |
---|
| 554 | end |
---|
| 555 | |
---|
| 556 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
---|
| 557 | for icell=1:length(CellInfo) |
---|
| 558 | if NbDim(icell)~=1 % skip field cells which are of dim 1 |
---|
| 559 | switch CellInfo{icell}.CoordType |
---|
| 560 | case 'scattered' %case of input fields with unstructured coordinates: just concatene data |
---|
| 561 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
---|
| 562 | VarName=Data{1}.ListVarName{ivar}; |
---|
| 563 | for iview=2:NbView |
---|
| 564 | MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
---|
| 565 | end |
---|
| 566 | end |
---|
| 567 | case 'grid' %case of fields defined on a structured grid |
---|
| 568 | FFName=''; |
---|
| 569 | if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) |
---|
| 570 | FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable |
---|
| 571 | MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) |
---|
| 572 | MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; |
---|
| 573 | MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; |
---|
| 574 | end |
---|
| 575 | % select good data on each view |
---|
| 576 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
---|
| 577 | VarName=Data{1}.ListVarName{ivar}; |
---|
| 578 | for iview=1:NbView |
---|
| 579 | if isempty(FFName) |
---|
| 580 | check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else |
---|
| 581 | else |
---|
| 582 | check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else |
---|
| 583 | end |
---|
| 584 | Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
---|
| 585 | if iview==1 |
---|
| 586 | %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field |
---|
| 587 | MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
---|
| 588 | NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point |
---|
| 589 | elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) |
---|
| 590 | errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; |
---|
| 591 | return |
---|
[1058] | 592 | else |
---|
[938] | 593 | MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data |
---|
| 594 | NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else |
---|
| 595 | end |
---|
| 596 | end |
---|
| 597 | MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point |
---|
| 598 | MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data |
---|
| 599 | end |
---|
| 600 | end |
---|
| 601 | end |
---|
[1058] | 602 | end |
---|