1 | %'time_series': extract a time series after projection on an object (points , line..) |
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2 | % this function can be used as a template for applying a global operation on a series of input fields |
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3 | %------------------------------------------------------------------------ |
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4 | % function GUI_input=time_series(Param) |
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5 | % |
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6 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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7 | % |
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8 | %OUTPUT |
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9 | % ParamOut: sets options in the GUI series.fig needed for the function |
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10 | % |
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11 | %INPUT: |
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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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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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16 | % |
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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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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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22 | % .OutputDirExt: directory extension for data outputs |
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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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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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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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33 | % .FieldName: name(s) of the field |
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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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37 | % .Coord_y: name of y coordinate variable |
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38 | % .Coord_x: name of x coordinate variable |
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39 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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40 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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41 | |
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42 | %======================================================================= |
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43 | % Copyright 2008-2015, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France |
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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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60 | function ParamOut=time_series(Param) |
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61 | |
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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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63 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
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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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69 | ParamOut.FieldTransform = 'on';%can use a transform function |
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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 | ParamOut.ProjObject='on';%can use projection object(option 'off'/'on', |
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72 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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73 | ParamOut.OutputDirExt='.tseries';%set the output dir extension |
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74 | 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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75 | % check for selection of a projection object |
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76 | hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series |
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77 | hhseries=guidata(hseries); |
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78 | if ~isfield(Param,'ProjObject') |
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79 | answer=msgbox_uvmat('INPUT_Y-N','use a projection object for the time_series?'); |
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80 | if strcmp(answer,'Yes') |
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81 | set(hhseries.CheckObject,'Visible','on') |
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82 | set(hhseries.CheckObject,'Value',1) |
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83 | series('CheckObject_Callback',hseries,[],hhseries); %file input with xml reading in uvmat, show the image in phys coordinates |
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84 | end |
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85 | end |
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86 | |
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87 | % introduce bin size for histograms |
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88 | if isfield(Param,'CheckObject') &&Param.CheckObject |
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89 | SeriesData=get(hseries,'UserData'); |
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90 | if ismember(SeriesData.ProjObject.ProjMode,{'inside','outside'}) |
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91 | answer=msgbox_uvmat('INPUT_TXT','set bin size for histograms (or keep ''auto'' by default)?','auto'); |
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92 | ParamOut.ActionInput.VarMesh=str2num(answer); |
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93 | end |
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94 | end |
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95 | |
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96 | % test for subtraction |
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97 | if size(Param.InputTable,1)>2 |
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98 | 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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99 | end |
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100 | if size(Param.InputTable,1)>=2 |
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101 | answer=msgbox_uvmat('INPUT_Y-N','substract the two input file series?'); |
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102 | if strcmp(answer,'Yes') |
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103 | if isempty(Param.FieldTransform.TransformName) |
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104 | set(hhseries.TransformName,'value',2) %select sub_field |
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105 | end |
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106 | else |
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107 | set(hhseries.InputTable,'Data',Param.InputTable(1,:)) |
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108 | end |
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109 | end |
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110 | |
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111 | % check the existence of the first and last file in the series |
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112 | first_j=[]; |
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113 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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114 | last_j=[]; |
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115 | if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end |
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116 | PairString=''; |
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117 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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118 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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119 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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120 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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121 | if ~exist(FirstFileName,'file') |
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122 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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123 | else |
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124 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); |
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125 | LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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126 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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127 | if ~exist(LastFileName,'file') |
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128 | msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) |
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129 | end |
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130 | end |
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131 | return |
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132 | end |
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133 | |
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134 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% |
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135 | ParamOut=[]; %default output |
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136 | %% read input parameters from an xml file if input is a file name (batch mode) |
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137 | checkrun=1; |
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138 | if ischar(Param) |
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139 | Param=xml2struct(Param);% read Param as input file (batch case) |
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140 | checkrun=0; |
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141 | end |
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142 | hseries=findobj(allchild(0),'Tag','series'); |
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143 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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144 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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145 | |
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146 | %% define the directory for result file (with path=RootPath{1}) |
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147 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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148 | |
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149 | %% root input file(s) name, type and index series |
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150 | RootPath=Param.InputTable(:,1); |
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151 | RootFile=Param.InputTable(:,3); |
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152 | SubDir=Param.InputTable(:,2); |
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153 | NomType=Param.InputTable(:,4); |
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154 | FileExt=Param.InputTable(:,5); |
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155 | hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); |
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156 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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157 | if ~isempty(hdisp),delete(hdisp),end; |
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158 | %%%%%%%%%%%% |
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159 | % The cell array filecell is the list of input file names, while |
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160 | % filecell{iview,fileindex}: |
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161 | % iview: line in the table corresponding to a given file series |
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162 | % fileindex: file index within the file series, |
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163 | % 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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164 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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165 | %%%%%%%%%%%% |
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166 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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167 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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168 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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169 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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170 | |
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171 | %% determine the file type on each line from the first input file |
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172 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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173 | NcTypeOptions={'netcdf','civx','civdata'}; |
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174 | FileType=cell(1,nbview); |
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175 | FileInfo=cell(1,nbview); |
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176 | MovieObject=cell(1,nbview); |
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177 | CheckImage=cell(1,nbview); |
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178 | CheckNc=cell(1,nbview); |
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179 | frame_index=cell(1,nbview); |
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180 | |
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181 | for iview=1:nbview |
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182 | if ~exist(filecell{iview,1}','file') |
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183 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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184 | return |
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185 | end |
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186 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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187 | FileType{iview}=FileInfo{iview}.FileType; |
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188 | if strcmp(FileType{iview},'civdata')||strcmp(FileType{iview},'civx') |
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189 | if ~isfield(Param.InputFields,'VelType') |
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190 | FileType{iview}='netcdf';% civ data read as usual netcdf files |
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191 | end |
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192 | end |
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193 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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194 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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195 | if isempty(j1_series{iview}) |
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196 | frame_index{iview}=i1_series{iview}; |
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197 | else |
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198 | frame_index{iview}=j1_series{iview}; |
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199 | end |
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200 | end |
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201 | |
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202 | %% calibration data and timing: read the ImaDoc files |
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203 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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204 | if ~isempty(errormsg) |
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205 | disp_uvmat('ERROR',['error in reading xmlfile: ' errormsg],checkrun) |
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206 | return |
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207 | end |
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208 | if size(time,1)>1 |
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209 | diff_time=max(max(diff(time))); |
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210 | if diff_time>0 |
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211 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) |
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212 | end |
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213 | time=time(1,:);% choose the time data from the first sequence |
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214 | end |
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215 | |
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216 | %% coordinate transform or other user defined transform |
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217 | transform_fct=[];%default |
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218 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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219 | addpath(Param.FieldTransform.TransformPath) |
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220 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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221 | rmpath(Param.FieldTransform.TransformPath) |
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222 | if isfield(Param,'TransformInput') |
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223 | XmlData{1}.TransformInput=Param.TransformInput; |
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224 | end |
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225 | end |
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226 | |
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227 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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228 | % EDIT FROM HERE |
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229 | |
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230 | %% check the validity of the input file types |
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231 | if ~CheckImage{1}&&~CheckNc{1} |
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232 | disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun) |
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233 | return |
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234 | end |
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235 | if nbview==2 && ~isequal(CheckImage{1},CheckImage{2}) |
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236 | disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun) |
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237 | return |
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238 | end |
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239 | |
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240 | %% settings for the output file |
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241 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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242 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file |
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243 | first_i=i1_series{1}(1); |
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244 | last_i=i1_series{1}(end); |
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245 | if isempty(j1_series{1})% if there is no second index j |
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246 | first_j=1;last_j=1; |
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247 | else |
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248 | first_j=j1_series{1}(1); |
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249 | last_j=j1_series{1}(end); |
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250 | end |
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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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254 | if nbview==2 |
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255 | InputFields{2}=[];%default (case of images) |
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256 | end |
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257 | if isfield(Param,'InputFields') |
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258 | InputFields{1}=Param.InputFields; |
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259 | if nbview==2 |
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260 | InputFields{2}=Param.InputFields;%default |
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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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269 | |
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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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272 | [DataOut,tild,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1); |
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273 | if ~isempty(errormsg) |
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274 | disp_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg],checkrun) |
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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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298 | nbfile=0;% not used , to check |
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299 | nbmissing=0; |
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300 | VarMesh=[]; |
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301 | checkhisto=0; |
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302 | if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}) |
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303 | checkhisto=1; |
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304 | if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms |
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305 | VarMesh=Param.ActionInput.VarMesh; |
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306 | else |
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307 | VarMesh=[]; |
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308 | disp_uvmat('WARNING','automatic bin size for histograms, select time_series again to set the value',checkrun) |
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309 | end |
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310 | end |
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311 | |
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312 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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313 | for index=1:nbfield |
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314 | update_waitbar(WaitbarHandle,index/nbfield) |
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315 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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316 | disp('program stopped by user') |
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317 | break % leave the loop if stop is ordered |
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318 | end |
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319 | Data=cell(1,nbview);%initiate the set Data; |
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320 | nbtime=0; |
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321 | dt=[]; |
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322 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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323 | for iview=1:nbview |
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324 | % reading input file(s) |
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325 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); |
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326 | if ~isempty(errormsg) |
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327 | errormsg=['time_series / read_field / ' errormsg]; |
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328 | disp(errormsg) |
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329 | break% exit the loop on iview |
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330 | end |
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331 | if ~isempty(NbSlice_calib) |
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332 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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333 | end |
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334 | end |
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335 | if ~isempty(errormsg) |
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336 | continue %in case of input error skip the current input field, go to next index |
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337 | end |
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338 | Field=Data{1}; % default input field structure |
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339 | % coordinate transform (or other user defined transform) |
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340 | if ~isempty(transform_fct) |
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341 | switch nargin(transform_fct) |
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342 | case 4 |
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343 | if length(Data)==2 |
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344 | Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); |
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345 | else |
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346 | Field=transform_fct(Data{1},XmlData{1}); |
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347 | end |
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348 | case 3 |
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349 | if length(Data)==2 |
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350 | Field=transform_fct(Data{1},XmlData{1},Data{2}); |
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351 | else |
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352 | Field=transform_fct(Data{1},XmlData{1}); |
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353 | end |
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354 | case 2 |
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355 | Field=transform_fct(Data{1},XmlData{1}); |
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356 | case 1 |
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357 | Field=transform_fct(Data{1}); |
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358 | end |
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359 | end |
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360 | |
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361 | %field projection on an object |
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362 | if Param.CheckObject |
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363 | % calculate tps coefficients if needed |
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364 | if isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps') |
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365 | Field=tps_coeff_field(Field,check_proj_tps); |
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366 | end |
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367 | [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh); |
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368 | if ~isempty(errormsg) |
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369 | disp_uvmat('ERROR',['time_series / proj_field / ' errormsg],checkrun) |
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370 | return |
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371 | end |
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372 | end |
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373 | % nbfile=nbfile+1; |
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374 | |
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375 | % initiate the time series at the first iteration |
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376 | if index==1 |
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377 | % stop program if the first field reading is in error |
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378 | if ~isempty(errormsg) |
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379 | disp_uvmat('ERROR',['time_series / sub_field / ' errormsg],checkrun) |
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380 | return |
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381 | end |
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382 | if ~isfield(Field,'ListVarName') |
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383 | disp_uvmat('ERROR','no variable in the projected field',checkrun) |
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384 | return |
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385 | end |
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386 | DataOut=Field;%output reproduced the first projected field by default |
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387 | nbvar=length(Field.ListVarName); |
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388 | if nbvar==0 |
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389 | disp_uvmat('ERROR','no input variable selected',checkrun) |
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390 | return |
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391 | end |
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392 | if checkhisto%case of histograms |
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393 | testsum=zeros(1,nbvar);%initiate flag for action on each variable |
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394 | for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram) |
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395 | VarName=Field.ListVarName{ivar}; |
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396 | if isfield(Data{1},VarName) |
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397 | DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Histo']}]; |
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398 | DataOut.VarDimName=[DataOut.VarDimName {{'Time',VarName}}]; |
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399 | % if isfield(DataOut.VarAttribute{ivar},'Role') |
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400 | % DataOut.VarAttribute{ivar}=rmfield(DataOut.VarAttribute{ivar},'Role'); |
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401 | % end |
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402 | StatName=pdf2stat;% get the names of statistical quantities to calcuilate at each time |
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403 | for istat=1:numel(StatName) |
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404 | DataOut.ListVarName=[DataOut.ListVarName {[VarName StatName{istat}]}]; |
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405 | DataOut.VarDimName=[DataOut.VarDimName {'Time'}]; |
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406 | end |
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407 | testsum(ivar)=1; |
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408 | DataOut.(VarName)=Field.(VarName); |
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409 | DataOut.([VarName 'Histo'])=zeros([nbfield numel(DataOut.(VarName))]); |
---|
410 | VarMesh=Field.(VarName)(2)-Field.(VarName)(1); |
---|
411 | end |
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412 | end |
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413 | disp(['mesh for histogram = ' num2str(VarMesh)]) |
---|
414 | else |
---|
415 | testsum=2*ones(1,nbvar);%initiate flag for action on each variable |
---|
416 | if isfield(Field,'VarAttribute') % look for coordinate and flag variables |
---|
417 | for ivar=1:nbvar |
---|
418 | if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role') |
---|
419 | var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable |
---|
420 | if isequal(var_role,'errorflag') |
---|
421 | disp_uvmat('ERROR','do not handle error flags in time series',checkrun) |
---|
422 | return |
---|
423 | end |
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424 | if isequal(var_role,'warnflag') |
---|
425 | testsum(ivar)=0; % not recorded variable |
---|
426 | eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable |
---|
427 | end |
---|
428 | if strcmp(var_role,'coord_x')||strcmp(var_role,'coord_y')||strcmp(var_role,'coord_z')||strcmp(var_role,'coord') |
---|
429 | testsum(ivar)=1; %constant coordinates, record without time evolution |
---|
430 | end |
---|
431 | end |
---|
432 | % check whether the variable ivar is a dimension variable |
---|
433 | DimCell=Field.VarDimName{ivar}; |
---|
434 | if ischar(DimCell) |
---|
435 | DimCell={DimCell}; |
---|
436 | end |
---|
437 | if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables |
---|
438 | testsum(ivar)=1; |
---|
439 | end |
---|
440 | end |
---|
441 | end |
---|
442 | for ivar=1:nbvar |
---|
443 | if testsum(ivar)==2 |
---|
444 | VarName=Field.ListVarName{ivar}; |
---|
445 | siz=size(Field.(VarName)); |
---|
446 | DataOut.(VarName)=zeros([nbfield siz]); |
---|
447 | end |
---|
448 | end |
---|
449 | end |
---|
450 | DataOut.ListVarName=[{'Time'} DataOut.ListVarName]; |
---|
451 | end |
---|
452 | % end initialisation for index==1 |
---|
453 | |
---|
454 | % append data from the current field |
---|
455 | |
---|
456 | if checkhisto % case of histogram (projection mode=inside or outside) |
---|
457 | for ivar=1:length(Field.ListVarName) |
---|
458 | VarName=Field.ListVarName{ivar}; |
---|
459 | if isfield(Data{1},VarName) |
---|
460 | MaxValue=max(DataOut.(VarName));% current max of histogram absissa |
---|
461 | MinValue=min(DataOut.(VarName));% current min of histogram absissa |
---|
462 | MaxIndex=round(MaxValue/VarMesh); |
---|
463 | MinIndex=round(MinValue/VarMesh); |
---|
464 | MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field |
---|
465 | MinIndex_new=round(min(Field.(VarName)/VarMesh)); |
---|
466 | if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one |
---|
467 | DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values |
---|
468 | DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(nbfield,MaxIndex_new-MaxIndex)]; % append the new histo values |
---|
469 | end |
---|
470 | if MinIndex_new <= MinIndex-1 |
---|
471 | DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values |
---|
472 | DataOut.([VarName 'Histo'])=[zeros(nbfield,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values |
---|
473 | ind_start=1; |
---|
474 | else |
---|
475 | ind_start=MinIndex_new-MinIndex+1; |
---|
476 | end |
---|
477 | DataOut.([VarName 'Histo'])(index,ind_start:ind_start+MaxIndex_new-MinIndex_new)=... |
---|
478 | DataOut.([VarName 'Histo'])(index,ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']); |
---|
479 | VarVal=pdf2stat((Field.(VarName))',(Field.([VarName 'Histo']))');% max of the current field |
---|
480 | for istat=1:numel(VarVal) |
---|
481 | DataOut.([VarName StatName{istat}])(index)=VarVal(istat); |
---|
482 | end |
---|
483 | end |
---|
484 | end |
---|
485 | else % not histogram |
---|
486 | for ivar=1:length(Field.ListVarName) |
---|
487 | VarName=Field.ListVarName{ivar}; |
---|
488 | VarVal=Field.(VarName); |
---|
489 | if testsum(ivar)==2% test for recorded variable |
---|
490 | if isempty(errormsg) |
---|
491 | VarVal=shiftdim(VarVal,-1); %shift dimension |
---|
492 | DataOut.(VarName)(index,:,:)=VarVal;%concanete the current field to the time series |
---|
493 | end |
---|
494 | elseif testsum(ivar)==1% variable representing fixed coordinates |
---|
495 | VarInit=DataOut.(VarName); |
---|
496 | if isempty(errormsg) && ~isequal(VarVal,VarInit) |
---|
497 | disp_uvmat('ERROR',['time series requires constant coordinates ' VarName ': use projection mode interp'],checkrun) |
---|
498 | return |
---|
499 | end |
---|
500 | end |
---|
501 | end |
---|
502 | end |
---|
503 | |
---|
504 | % record the time: |
---|
505 | if isempty(time)% time not set by xml filer(s) |
---|
506 | if isfield(Data{1},'Time') |
---|
507 | DataOut.Time(index,1)=Field.Time; |
---|
508 | else |
---|
509 | DataOut.Time(index,1)=index;%default |
---|
510 | end |
---|
511 | else % time from ImaDoc prevails TODO: correct |
---|
512 | DataOut.Time(index,1)=time(index);% |
---|
513 | end |
---|
514 | index |
---|
515 | % record the number of missing input fields |
---|
516 | if ~isempty(errormsg) |
---|
517 | nbmissing=nbmissing+1; |
---|
518 | display(['index=' num2str(index) ':' errormsg]) |
---|
519 | end |
---|
520 | end |
---|
521 | |
---|
522 | %%%%%%% END OF LOOP WITHIN A SLICE |
---|
523 | |
---|
524 | %remove time for global attributes if exists |
---|
525 | Time_index=find(strcmp('Time',DataOut.ListGlobalAttribute)); |
---|
526 | if ~isempty(Time_index) |
---|
527 | DataOut.ListGlobalAttribute(Time_index)=[]; |
---|
528 | end |
---|
529 | DataOut.Conventions='uvmat'; |
---|
530 | for ivar=1:numel(DataOut.ListVarName) |
---|
531 | VarName=DataOut.ListVarName{ivar}; |
---|
532 | eval(['DataOut.' VarName '=squeeze(DataOut.' VarName ');']) %remove singletons |
---|
533 | end |
---|
534 | |
---|
535 | % add time dimension |
---|
536 | for ivar=1:length(Field.ListVarName) |
---|
537 | DimCell=Field.VarDimName{ivar}; |
---|
538 | if ischar(DimCell),DimCell={DimCell};end |
---|
539 | if testsum(ivar)==2% variable for which time series is calculated |
---|
540 | DataOut.VarDimName{ivar}=[{'Time'} DimCell]; |
---|
541 | elseif testsum(ivar)==1 % variable represneting a fixed coordinate |
---|
542 | DataOut.VarDimName{ivar}=DimCell; |
---|
543 | end |
---|
544 | end |
---|
545 | indexremove=find(~testsum); |
---|
546 | if ~isempty(indexremove) |
---|
547 | DataOut.ListVarName(1+indexremove)=[]; |
---|
548 | DataOut.VarDimName(indexremove)=[]; |
---|
549 | if isfield(DataOut,'Role') && ~isempty(DataOut.Role{1})%generaliser aus autres attributs |
---|
550 | DataOut.Role(1+indexremove)=[]; |
---|
551 | end |
---|
552 | end |
---|
553 | |
---|
554 | %shift variable attributes |
---|
555 | if isfield(DataOut,'VarAttribute') |
---|
556 | DataOut.VarAttribute=[{[]} DataOut.VarAttribute]; |
---|
557 | end |
---|
558 | DataOut.VarDimName=[{'Time'} DataOut.VarDimName]; |
---|
559 | DataOut.Action=Param.Action;%name of the processing programme |
---|
560 | test_time=diff(DataOut.Time)>0;% test that the readed time is increasing (not constant) |
---|
561 | if ~test_time |
---|
562 | DataOut.Time=1:nbfield; |
---|
563 | end |
---|
564 | |
---|
565 | % %case of histograms |
---|
566 | % if checkhisto |
---|
567 | % for ivar=1:numel(Field.ListVarName) |
---|
568 | % VarName=Field.ListVarName{ivar}; |
---|
569 | % if isfield(Data{1},VarName) |
---|
570 | % DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Histo']}]; |
---|
571 | % DataOut.VarDimName=[DataOut.VarDimName {{'Time',VarName}}]; |
---|
572 | % end |
---|
573 | % end |
---|
574 | % end |
---|
575 | % display nbmissing |
---|
576 | if ~isequal(nbmissing,0) |
---|
577 | disp_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'],checkrun) |
---|
578 | end |
---|
579 | |
---|
580 | %% name of result file |
---|
581 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); |
---|
582 | errormsg=struct2nc(OutputFile,DataOut); %save result file |
---|
583 | if isempty(errormsg) |
---|
584 | display([OutputFile ' written']) |
---|
585 | else |
---|
586 | disp_uvmat('ERROR',['error in Series/struct2nc: ' errormsg],checkrun) |
---|
587 | end |
---|
588 | |
---|
589 | %% plot the time series for (the last one in case of multislices) |
---|
590 | if checkrun %&& isfield(Param,'ProjObject') && strcmp(Param.ProjObject.Type,'points') |
---|
591 | %% open the result file with uvmat (in RUN mode) |
---|
592 | uvmat(OutputFile)% open the last result file with uvmat |
---|
593 | end |
---|
594 | % figure |
---|
595 | % haxes=axes; |
---|
596 | % plot_field(DataOut,haxes) |
---|
597 | % |
---|
598 | % %% display the result file using the GUI get_field |
---|
599 | % hget_field=findobj(allchild(0),'name','get_field'); |
---|
600 | % if ~isempty(hget_field) |
---|
601 | % delete(hget_field) |
---|
602 | % end |
---|
603 | % get_field(OutputFile,DataOut) |
---|
604 | % end |
---|
605 | |
---|
606 | |
---|