[572] | 1 | %'time_series': extract a time series after projection on an object (points , line..) |
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[457] | 2 | % this function can be used as a template for applying a global operation on a series of input fields |
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[169] | 3 | %------------------------------------------------------------------------ |
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[374] | 4 | % function GUI_input=time_series(Param) |
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[169] | 5 | % |
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[457] | 6 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 7 | % |
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[169] | 8 | %OUTPUT |
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[596] | 9 | % ParamOut: sets options in the GUI series.fig needed for the function |
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[169] | 10 | % |
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| 11 | %INPUT: |
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[457] | 12 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 13 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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[596] | 14 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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| 15 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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[169] | 16 | % |
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[596] | 17 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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| 18 | % see the current structure Param) |
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[457] | 19 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 20 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 21 | % .OutputSubDir: name of the subdirectory for data outputs |
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[474] | 22 | % .OutputDirExt: directory extension for data outputs |
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[457] | 23 | % .Action: .ActionName: name of the current activated function |
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| 24 | % .ActionPath: path of the current activated function |
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[596] | 25 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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| 26 | % .RUN =0 for GUI input, =1 for function activation |
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| 27 | % .RunMode='local','background', 'cluster': type of function use |
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| 28 | % |
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[457] | 29 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 30 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 31 | % .TransformPath: path of the selected transform function |
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| 32 | % .InputFields: sub structure describing the input fields withfields |
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[596] | 33 | % .FieldName: name(s) of the field |
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[457] | 34 | % .VelType: velocity type |
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| 35 | % .FieldName_1: name of the second field in case of two input series |
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| 36 | % .VelType_1: velocity type of the second field in case of two input series |
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[596] | 37 | % .Coord_y: name of y coordinate variable |
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| 38 | % .Coord_x: name of x coordinate variable |
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[457] | 39 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 40 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[596] | 41 | |
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[810] | 42 | %======================================================================= |
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[1093] | 43 | % Copyright 2008-2021, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[810] | 44 | % http://www.legi.grenoble-inp.fr |
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| 45 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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| 46 | % |
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| 47 | % This file is part of the toolbox UVMAT. |
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| 48 | % |
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| 49 | % UVMAT is free software; you can redistribute it and/or modify |
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| 50 | % it under the terms of the GNU General Public License as published |
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| 51 | % by the Free Software Foundation; either version 2 of the license, |
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| 52 | % or (at your option) any later version. |
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| 53 | % |
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| 54 | % UVMAT is distributed in the hope that it will be useful, |
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| 55 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 56 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 57 | % GNU General Public License (see LICENSE.txt) for more details. |
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| 58 | %======================================================================= |
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| 59 | |
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[457] | 60 | function ParamOut=time_series(Param) |
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[27] | 61 | |
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[606] | 62 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed |
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[875] | 63 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
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[605] | 64 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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| 65 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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| 66 | ParamOut.NbSlice='on'; %nbre of slices ('off' by default) |
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| 67 | ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 68 | ParamOut.FieldName='two';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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[1001] | 69 | ParamOut.FieldTransform = {'phys','phys_polar'};%can use a transform function, proposed list (needed for compilation) |
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| 70 | ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) |
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| 71 | if 1==2 % loop used to enforce compilation of transform fct, never entered. |
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| 72 | phys |
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| 73 | phys_polar |
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| 74 | end |
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[605] | 75 | ParamOut.ProjObject='on';%can use projection object(option 'off'/'on', |
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| 76 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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| 77 | ParamOut.OutputDirExt='.tseries';%set the output dir extension |
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| 78 | ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice |
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[871] | 79 | % check for selection of a projection object |
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| 80 | hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series |
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[875] | 81 | hhseries=guidata(hseries); |
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[871] | 82 | if ~isfield(Param,'ProjObject') |
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[1085] | 83 | msgbox_uvmat('WARNING','you may need to introduce a projection object for the time_series'); |
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[871] | 84 | end |
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[875] | 85 | |
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[871] | 86 | % introduce bin size for histograms |
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[872] | 87 | if isfield(Param,'CheckObject') &&Param.CheckObject |
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[871] | 88 | SeriesData=get(hseries,'UserData'); |
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[872] | 89 | if ismember(SeriesData.ProjObject.ProjMode,{'inside','outside'}) |
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[875] | 90 | answer=msgbox_uvmat('INPUT_TXT','set bin size for histograms (or keep ''auto'' by default)?','auto'); |
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[880] | 91 | ParamOut.ActionInput.VarMesh=str2num(answer); |
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[871] | 92 | end |
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| 93 | end |
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[875] | 94 | |
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[874] | 95 | % test for subtraction |
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[875] | 96 | if size(Param.InputTable,1)>2 |
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| 97 | msgbox_uvmat('WARNING','''time_series'' uses only one or two input lines (two for substraction). To concatene fields first use ''merge_proj'''); |
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| 98 | end |
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| 99 | if size(Param.InputTable,1)>=2 |
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| 100 | answer=msgbox_uvmat('INPUT_Y-N','substract the two input file series?'); |
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| 101 | if strcmp(answer,'Yes') |
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| 102 | if isempty(Param.FieldTransform.TransformName) |
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| 103 | set(hhseries.TransformName,'value',2) %select sub_field |
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| 104 | end |
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| 105 | else |
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| 106 | set(hhseries.InputTable,'Data',Param.InputTable(1,:)) |
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[874] | 107 | end |
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[875] | 108 | end |
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| 109 | |
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[871] | 110 | % check the existence of the first and last file in the series |
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[875] | 111 | first_j=[]; |
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[716] | 112 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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| 113 | last_j=[]; |
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| 114 | if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end |
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| 115 | PairString=''; |
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| 116 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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| 117 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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| 118 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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| 119 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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| 120 | if ~exist(FirstFileName,'file') |
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| 121 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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[871] | 122 | else |
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| 123 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); |
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| 124 | LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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| 125 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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| 126 | if ~exist(LastFileName,'file') |
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| 127 | msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) |
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| 128 | end |
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[605] | 129 | end |
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[599] | 130 | return |
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[27] | 131 | end |
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| 132 | |
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[526] | 133 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% |
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[624] | 134 | ParamOut=[]; %default output |
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[592] | 135 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 136 | checkrun=1; |
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[457] | 137 | if ischar(Param) |
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[592] | 138 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 139 | checkrun=0; |
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[374] | 140 | end |
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[624] | 141 | hseries=findobj(allchild(0),'Tag','series'); |
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| 142 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 143 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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[592] | 144 | |
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[624] | 145 | %% define the directory for result file (with path=RootPath{1}) |
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[474] | 146 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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[457] | 147 | |
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[609] | 148 | %% root input file(s) name, type and index series |
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[457] | 149 | RootPath=Param.InputTable(:,1); |
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| 150 | RootFile=Param.InputTable(:,3); |
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| 151 | SubDir=Param.InputTable(:,2); |
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| 152 | NomType=Param.InputTable(:,4); |
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| 153 | FileExt=Param.InputTable(:,5); |
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[960] | 154 | |
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[751] | 155 | hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); |
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[960] | 156 | % gives the series of input file names and indices set by the input parameters: |
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[374] | 157 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[526] | 158 | % filecell{iview,fileindex}: |
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[457] | 159 | % iview: line in the table corresponding to a given file series |
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[960] | 160 | % fileindex: file index with i and j reshaped as a 1D array |
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| 161 | % 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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[457] | 162 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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[960] | 163 | if ~isempty(hdisp),delete(hdisp),end;%end the waiting display |
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[374] | 164 | |
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[960] | 165 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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| 166 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 167 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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| 168 | NbField=NbField_j*NbField_i; %total number of fields |
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| 169 | |
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[609] | 170 | %% determine the file type on each line from the first input file |
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[984] | 171 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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[457] | 172 | NcTypeOptions={'netcdf','civx','civdata'}; |
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[970] | 173 | FileType=cell(1,NbView); |
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| 174 | FileInfo=cell(1,NbView); |
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| 175 | MovieObject=cell(1,NbView); |
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| 176 | CheckImage=cell(1,NbView); |
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| 177 | CheckNc=cell(1,NbView); |
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| 178 | frame_index=cell(1,NbView); |
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[874] | 179 | |
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[970] | 180 | for iview=1:NbView |
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[457] | 181 | if ~exist(filecell{iview,1}','file') |
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[668] | 182 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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[27] | 183 | return |
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| 184 | end |
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[784] | 185 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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[783] | 186 | FileType{iview}=FileInfo{iview}.FileType; |
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[768] | 187 | if strcmp(FileType{iview},'civdata')||strcmp(FileType{iview},'civx') |
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| 188 | if ~isfield(Param.InputFields,'VelType') |
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| 189 | FileType{iview}='netcdf';% civ data read as usual netcdf files |
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| 190 | end |
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| 191 | end |
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[457] | 192 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 193 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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[768] | 194 | if isempty(j1_series{iview}) |
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| 195 | frame_index{iview}=i1_series{iview}; |
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| 196 | else |
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[457] | 197 | frame_index{iview}=j1_series{iview}; |
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| 198 | end |
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[27] | 199 | end |
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| 200 | |
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[457] | 201 | %% calibration data and timing: read the ImaDoc files |
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[470] | 202 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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[768] | 203 | if ~isempty(errormsg) |
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| 204 | disp_uvmat('ERROR',['error in reading xmlfile: ' errormsg],checkrun) |
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| 205 | return |
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| 206 | end |
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[470] | 207 | if size(time,1)>1 |
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[457] | 208 | diff_time=max(max(diff(time))); |
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| 209 | if diff_time>0 |
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[668] | 210 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) |
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[599] | 211 | end |
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[531] | 212 | time=time(1,:);% choose the time data from the first sequence |
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[457] | 213 | end |
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[27] | 214 | |
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[457] | 215 | %% coordinate transform or other user defined transform |
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[526] | 216 | transform_fct=[];%default |
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[478] | 217 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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[1001] | 218 | %addpath(Param.FieldTransform.TransformPath) |
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[474] | 219 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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[1001] | 220 | %rmpath(Param.FieldTransform.TransformPath) |
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[883] | 221 | if isfield(Param,'TransformInput') |
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| 222 | XmlData{1}.TransformInput=Param.TransformInput; |
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| 223 | end |
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[457] | 224 | end |
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[474] | 225 | |
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[457] | 226 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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[599] | 227 | % EDIT FROM HERE |
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[27] | 228 | |
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[656] | 229 | %% check the validity of the input file types |
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| 230 | if ~CheckImage{1}&&~CheckNc{1} |
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[668] | 231 | disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun) |
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[457] | 232 | return |
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[27] | 233 | end |
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[970] | 234 | if NbView==2 && ~isequal(CheckImage{1},CheckImage{2}) |
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[668] | 235 | disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun) |
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[259] | 236 | return |
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| 237 | end |
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[635] | 238 | |
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| 239 | %% settings for the output file |
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[656] | 240 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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[609] | 241 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file |
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[635] | 242 | first_i=i1_series{1}(1); |
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| 243 | last_i=i1_series{1}(end); |
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| 244 | if isempty(j1_series{1})% if there is no second index j |
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| 245 | first_j=1;last_j=1; |
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| 246 | else |
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| 247 | first_j=j1_series{1}(1); |
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| 248 | last_j=j1_series{1}(end); |
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| 249 | end |
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[1091] | 250 | OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device) |
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[457] | 251 | |
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| 252 | %% Set field names and velocity types |
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| 253 | InputFields{1}=[];%default (case of images) |
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[970] | 254 | if NbView==2 |
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[867] | 255 | InputFields{2}=[];%default (case of images) |
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| 256 | end |
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[457] | 257 | if isfield(Param,'InputFields') |
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| 258 | InputFields{1}=Param.InputFields; |
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[970] | 259 | if NbView==2 |
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[867] | 260 | InputFields{2}=Param.InputFields;%default |
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[457] | 261 | if isfield(Param.InputFields,'FieldName_1') |
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| 262 | InputFields{2}.FieldName=Param.InputFields.FieldName_1; |
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| 263 | if isfield(Param.InputFields,'VelType_1') |
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| 264 | InputFields{2}.VelType=Param.InputFields.VelType_1; |
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| 265 | end |
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| 266 | end |
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| 267 | end |
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| 268 | end |
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[27] | 269 | |
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[457] | 270 | %% Initiate output fields |
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| 271 | %initiate the output structure as a copy of the first input one (reproduce fields) |
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[464] | 272 | [DataOut,tild,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1); |
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[457] | 273 | if ~isempty(errormsg) |
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[668] | 274 | disp_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg],checkrun) |
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[457] | 275 | return |
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| 276 | end |
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| 277 | time_1=[]; |
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| 278 | if isfield(DataOut,'Time') |
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| 279 | time_1=DataOut.Time(1); |
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| 280 | end |
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| 281 | if CheckNc{iview} |
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| 282 | if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute)) |
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| 283 | DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute]; |
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| 284 | end |
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| 285 | DataOut.Conventions='uvmat'; |
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| 286 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}]; |
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| 287 | ActionKey='Action'; |
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| 288 | while isfield(DataOut,ActionKey) |
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| 289 | ActionKey=[ActionKey '_1']; |
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| 290 | end |
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| 291 | DataOut.(ActionKey)=Param.Action; |
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| 292 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}]; |
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| 293 | if isfield(DataOut,'Time') |
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| 294 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}]; |
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| 295 | end |
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| 296 | end |
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| 297 | |
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[871] | 298 | nbfile=0;% not used , to check |
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[599] | 299 | nbmissing=0; |
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[880] | 300 | VarMesh=[]; |
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[871] | 301 | checkhisto=0; |
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[1069] | 302 | checkline=0; |
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| 303 | if isfield(Param,'ProjObject') |
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| 304 | if ismember(Param.ProjObject.ProjMode,{'inside','outside'}) |
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[871] | 305 | checkhisto=1; |
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[880] | 306 | if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms |
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| 307 | VarMesh=Param.ActionInput.VarMesh; |
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[1091] | 308 | elseif isequal(Param.IndexRange.NbSlice,1) |
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[884] | 309 | VarMesh=[]; |
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| 310 | disp_uvmat('WARNING','automatic bin size for histograms, select time_series again to set the value',checkrun) |
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[871] | 311 | end |
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[1069] | 312 | elseif ismember(Param.ProjObject.Type,{'line'}) |
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| 313 | checkline=1; |
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| 314 | end |
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[871] | 315 | end |
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[875] | 316 | |
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[599] | 317 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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[970] | 318 | for index=1:NbField |
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| 319 | update_waitbar(WaitbarHandle,index/NbField) |
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[635] | 320 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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[624] | 321 | disp('program stopped by user') |
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| 322 | break % leave the loop if stop is ordered |
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[599] | 323 | end |
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[970] | 324 | Data=cell(1,NbView);%initiate the set Data; |
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[599] | 325 | nbtime=0; |
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| 326 | dt=[]; |
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| 327 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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[970] | 328 | for iview=1:NbView |
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[599] | 329 | % reading input file(s) |
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| 330 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); |
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| 331 | if ~isempty(errormsg) |
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| 332 | errormsg=['time_series / read_field / ' errormsg]; |
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[880] | 333 | disp(errormsg) |
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| 334 | break% exit the loop on iview |
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[442] | 335 | end |
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[599] | 336 | if ~isempty(NbSlice_calib) |
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| 337 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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| 338 | end |
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| 339 | end |
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[880] | 340 | if ~isempty(errormsg) |
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| 341 | continue %in case of input error skip the current input field, go to next index |
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| 342 | end |
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| 343 | Field=Data{1}; % default input field structure |
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| 344 | % coordinate transform (or other user defined transform) |
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| 345 | if ~isempty(transform_fct) |
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| 346 | switch nargin(transform_fct) |
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| 347 | case 4 |
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| 348 | if length(Data)==2 |
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| 349 | Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); |
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| 350 | else |
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[875] | 351 | Field=transform_fct(Data{1},XmlData{1}); |
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[880] | 352 | end |
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| 353 | case 3 |
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| 354 | if length(Data)==2 |
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| 355 | Field=transform_fct(Data{1},XmlData{1},Data{2}); |
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| 356 | else |
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| 357 | Field=transform_fct(Data{1},XmlData{1}); |
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| 358 | end |
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| 359 | case 2 |
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| 360 | Field=transform_fct(Data{1},XmlData{1}); |
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| 361 | case 1 |
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| 362 | Field=transform_fct(Data{1}); |
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[599] | 363 | end |
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[880] | 364 | end |
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| 365 | |
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| 366 | %field projection on an object |
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| 367 | if Param.CheckObject |
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| 368 | % calculate tps coefficients if needed |
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| 369 | if isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps') |
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| 370 | Field=tps_coeff_field(Field,check_proj_tps); |
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[599] | 371 | end |
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[880] | 372 | [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh); |
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| 373 | if ~isempty(errormsg) |
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| 374 | disp_uvmat('ERROR',['time_series / proj_field / ' errormsg],checkrun) |
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| 375 | return |
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| 376 | end |
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| 377 | end |
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| 378 | % nbfile=nbfile+1; |
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| 379 | |
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| 380 | % initiate the time series at the first iteration |
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| 381 | if index==1 |
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| 382 | % stop program if the first field reading is in error |
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| 383 | if ~isempty(errormsg) |
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| 384 | disp_uvmat('ERROR',['time_series / sub_field / ' errormsg],checkrun) |
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| 385 | return |
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| 386 | end |
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| 387 | if ~isfield(Field,'ListVarName') |
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| 388 | disp_uvmat('ERROR','no variable in the projected field',checkrun) |
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| 389 | return |
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| 390 | end |
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| 391 | DataOut=Field;%output reproduced the first projected field by default |
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| 392 | nbvar=length(Field.ListVarName); |
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| 393 | if nbvar==0 |
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| 394 | disp_uvmat('ERROR','no input variable selected',checkrun) |
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| 395 | return |
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| 396 | end |
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| 397 | if checkhisto%case of histograms |
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| 398 | testsum=zeros(1,nbvar);%initiate flag for action on each variable |
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| 399 | for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram) |
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| 400 | VarName=Field.ListVarName{ivar}; |
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| 401 | if isfield(Data{1},VarName) |
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| 402 | DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Histo']}]; |
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| 403 | DataOut.VarDimName=[DataOut.VarDimName {{'Time',VarName}}]; |
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| 404 | StatName=pdf2stat;% get the names of statistical quantities to calcuilate at each time |
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| 405 | for istat=1:numel(StatName) |
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| 406 | DataOut.ListVarName=[DataOut.ListVarName {[VarName StatName{istat}]}]; |
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| 407 | DataOut.VarDimName=[DataOut.VarDimName {'Time'}]; |
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[871] | 408 | end |
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[880] | 409 | testsum(ivar)=1; |
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| 410 | DataOut.(VarName)=Field.(VarName); |
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[970] | 411 | DataOut.([VarName 'Histo'])=zeros([NbField numel(DataOut.(VarName))]); |
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[880] | 412 | VarMesh=Field.(VarName)(2)-Field.(VarName)(1); |
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[871] | 413 | end |
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[880] | 414 | end |
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| 415 | disp(['mesh for histogram = ' num2str(VarMesh)]) |
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| 416 | else |
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| 417 | testsum=2*ones(1,nbvar);%initiate flag for action on each variable |
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| 418 | if isfield(Field,'VarAttribute') % look for coordinate and flag variables |
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| 419 | for ivar=1:nbvar |
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| 420 | if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role') |
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| 421 | var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable |
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| 422 | if isequal(var_role,'errorflag') |
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| 423 | disp_uvmat('ERROR','do not handle error flags in time series',checkrun) |
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| 424 | return |
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[27] | 425 | end |
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[880] | 426 | if isequal(var_role,'warnflag') |
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| 427 | testsum(ivar)=0; % not recorded variable |
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| 428 | eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable |
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[27] | 429 | end |
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[1069] | 430 | if strcmp(var_role,'coord_x')||strcmp(var_role,'coord_z')||strcmp(var_role,'coord') |
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[880] | 431 | testsum(ivar)=1; %constant coordinates, record without time evolution |
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[474] | 432 | end |
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[1069] | 433 | if strcmp(var_role,'coord_y')&& ~checkline |
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| 434 | testsum(ivar)=1; |
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| 435 | end |
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[27] | 436 | end |
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[880] | 437 | % check whether the variable ivar is a dimension variable |
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| 438 | DimCell=Field.VarDimName{ivar}; |
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| 439 | if ischar(DimCell) |
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| 440 | DimCell={DimCell}; |
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[474] | 441 | end |
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[880] | 442 | if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables |
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| 443 | testsum(ivar)=1; |
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| 444 | end |
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[474] | 445 | end |
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| 446 | end |
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[880] | 447 | for ivar=1:nbvar |
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| 448 | if testsum(ivar)==2 |
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| 449 | VarName=Field.ListVarName{ivar}; |
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| 450 | siz=size(Field.(VarName)); |
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[970] | 451 | DataOut.(VarName)=zeros([NbField siz]); |
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[330] | 452 | end |
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[871] | 453 | end |
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[880] | 454 | end |
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| 455 | DataOut.ListVarName=[{'Time'} DataOut.ListVarName]; |
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| 456 | end |
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| 457 | % end initialisation for index==1 |
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| 458 | |
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| 459 | % append data from the current field |
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| 460 | |
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| 461 | if checkhisto % case of histogram (projection mode=inside or outside) |
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| 462 | for ivar=1:length(Field.ListVarName) |
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| 463 | VarName=Field.ListVarName{ivar}; |
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| 464 | if isfield(Data{1},VarName) |
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| 465 | MaxValue=max(DataOut.(VarName));% current max of histogram absissa |
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| 466 | MinValue=min(DataOut.(VarName));% current min of histogram absissa |
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| 467 | MaxIndex=round(MaxValue/VarMesh); |
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| 468 | MinIndex=round(MinValue/VarMesh); |
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| 469 | MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field |
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| 470 | MinIndex_new=round(min(Field.(VarName)/VarMesh)); |
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| 471 | if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one |
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| 472 | DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values |
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[970] | 473 | DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(NbField,MaxIndex_new-MaxIndex)]; % append the new histo values |
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[599] | 474 | end |
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[880] | 475 | if MinIndex_new <= MinIndex-1 |
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| 476 | DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values |
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[970] | 477 | DataOut.([VarName 'Histo'])=[zeros(NbField,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values |
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[880] | 478 | ind_start=1; |
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| 479 | else |
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| 480 | ind_start=MinIndex_new-MinIndex+1; |
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| 481 | end |
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| 482 | DataOut.([VarName 'Histo'])(index,ind_start:ind_start+MaxIndex_new-MinIndex_new)=... |
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| 483 | DataOut.([VarName 'Histo'])(index,ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']); |
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[881] | 484 | VarVal=pdf2stat((Field.(VarName))',(Field.([VarName 'Histo']))');% max of the current field |
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[880] | 485 | for istat=1:numel(VarVal) |
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| 486 | DataOut.([VarName StatName{istat}])(index)=VarVal(istat); |
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| 487 | end |
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[27] | 488 | end |
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[599] | 489 | end |
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[880] | 490 | else % not histogram |
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| 491 | for ivar=1:length(Field.ListVarName) |
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| 492 | VarName=Field.ListVarName{ivar}; |
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| 493 | VarVal=Field.(VarName); |
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| 494 | if testsum(ivar)==2% test for recorded variable |
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| 495 | if isempty(errormsg) |
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| 496 | VarVal=shiftdim(VarVal,-1); %shift dimension |
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| 497 | DataOut.(VarName)(index,:,:)=VarVal;%concanete the current field to the time series |
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| 498 | end |
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| 499 | elseif testsum(ivar)==1% variable representing fixed coordinates |
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| 500 | VarInit=DataOut.(VarName); |
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| 501 | if isempty(errormsg) && ~isequal(VarVal,VarInit) |
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| 502 | disp_uvmat('ERROR',['time series requires constant coordinates ' VarName ': use projection mode interp'],checkrun) |
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| 503 | return |
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| 504 | end |
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[474] | 505 | end |
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[27] | 506 | end |
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[880] | 507 | end |
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| 508 | |
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| 509 | % record the time: |
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| 510 | if isempty(time)% time not set by xml filer(s) |
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| 511 | if isfield(Data{1},'Time') |
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| 512 | DataOut.Time(index,1)=Field.Time; |
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| 513 | else |
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| 514 | DataOut.Time(index,1)=index;%default |
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[27] | 515 | end |
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[880] | 516 | else % time from ImaDoc prevails TODO: correct |
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| 517 | DataOut.Time(index,1)=time(index);% |
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[330] | 518 | end |
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[881] | 519 | index |
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[880] | 520 | % record the number of missing input fields |
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| 521 | if ~isempty(errormsg) |
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| 522 | nbmissing=nbmissing+1; |
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| 523 | display(['index=' num2str(index) ':' errormsg]) |
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| 524 | end |
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[599] | 525 | end |
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[880] | 526 | |
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[599] | 527 | %%%%%%% END OF LOOP WITHIN A SLICE |
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| 528 | |
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| 529 | %remove time for global attributes if exists |
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| 530 | Time_index=find(strcmp('Time',DataOut.ListGlobalAttribute)); |
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| 531 | if ~isempty(Time_index) |
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| 532 | DataOut.ListGlobalAttribute(Time_index)=[]; |
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| 533 | end |
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| 534 | DataOut.Conventions='uvmat'; |
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| 535 | for ivar=1:numel(DataOut.ListVarName) |
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| 536 | VarName=DataOut.ListVarName{ivar}; |
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| 537 | eval(['DataOut.' VarName '=squeeze(DataOut.' VarName ');']) %remove singletons |
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| 538 | end |
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| 539 | |
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| 540 | % add time dimension |
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| 541 | for ivar=1:length(Field.ListVarName) |
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[751] | 542 | DimCell=Field.VarDimName{ivar}; |
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| 543 | if ischar(DimCell),DimCell={DimCell};end |
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| 544 | if testsum(ivar)==2% variable for which time series is calculated |
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[599] | 545 | DataOut.VarDimName{ivar}=[{'Time'} DimCell]; |
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[751] | 546 | elseif testsum(ivar)==1 % variable represneting a fixed coordinate |
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[599] | 547 | DataOut.VarDimName{ivar}=DimCell; |
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[330] | 548 | end |
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[599] | 549 | end |
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| 550 | indexremove=find(~testsum); |
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| 551 | if ~isempty(indexremove) |
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| 552 | DataOut.ListVarName(1+indexremove)=[]; |
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| 553 | DataOut.VarDimName(indexremove)=[]; |
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| 554 | if isfield(DataOut,'Role') && ~isempty(DataOut.Role{1})%generaliser aus autres attributs |
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| 555 | DataOut.Role(1+indexremove)=[]; |
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[330] | 556 | end |
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[27] | 557 | end |
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[107] | 558 | |
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[599] | 559 | %shift variable attributes |
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| 560 | if isfield(DataOut,'VarAttribute') |
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| 561 | DataOut.VarAttribute=[{[]} DataOut.VarAttribute]; |
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| 562 | end |
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| 563 | DataOut.VarDimName=[{'Time'} DataOut.VarDimName]; |
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| 564 | DataOut.Action=Param.Action;%name of the processing programme |
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| 565 | test_time=diff(DataOut.Time)>0;% test that the readed time is increasing (not constant) |
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| 566 | if ~test_time |
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[970] | 567 | DataOut.Time=1:NbField; |
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[599] | 568 | end |
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| 569 | |
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| 570 | if ~isequal(nbmissing,0) |
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[668] | 571 | disp_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'],checkrun) |
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[599] | 572 | end |
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| 573 | |
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[609] | 574 | %% name of result file |
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[1091] | 575 | OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); |
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[599] | 576 | errormsg=struct2nc(OutputFile,DataOut); %save result file |
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| 577 | if isempty(errormsg) |
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| 578 | display([OutputFile ' written']) |
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| 579 | else |
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[668] | 580 | disp_uvmat('ERROR',['error in Series/struct2nc: ' errormsg],checkrun) |
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[599] | 581 | end |
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| 582 | |
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[880] | 583 | %% plot the time series for (the last one in case of multislices) |
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[1091] | 584 | if checkrun && isequal(Param.IndexRange.NbSlice,1)%&& isfield(Param,'ProjObject') && strcmp(Param.ProjObject.Type,'points') |
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[880] | 585 | %% open the result file with uvmat (in RUN mode) |
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| 586 | uvmat(OutputFile)% open the last result file with uvmat |
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[474] | 587 | end |
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[27] | 588 | |
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| 589 | |
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[1091] | 590 | |
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