[8] | 1 | %'imadoc2struct': reads the xml file for image documentation
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[89] | 2 | %------------------------------------------------------------------------
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[109] | 3 | % function [s,errormsg]=imadoc2struct(ImaDoc,option)
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[8] | 4 | %
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| 5 | % OUTPUT:
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| 6 | % s: structure representing ImaDoc
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| 7 | % s.Heading: information about the data hierarchical structure
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[611] | 8 | % s.Time: matrix of times, note that s.Time(i+1,j+1) is the time for file indices i and j (in order to deal with index 0)
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[8] | 9 | % s.TimeUnit
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| 10 | % s.GeometryCalib: substructure containing the parameters for geometric calibration
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| 11 | % errormsg: error message
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| 12 | %
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| 13 | % INPUT:
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| 14 | % ImaDoc: full name of the xml input file with head key ImaDoc
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[560] | 15 | % varargin: optional list of strings to restrict the reading to a selection of subtrees, for instance 'GeometryCalib' (save time)
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[89] | 16 |
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[809] | 17 | %=======================================================================
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[1061] | 18 | % Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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[809] | 19 | % http://www.legi.grenoble-inp.fr
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| 20 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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| 21 | %
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| 22 | % This file is part of the toolbox UVMAT.
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| 23 | %
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| 24 | % UVMAT is free software; you can redistribute it and/or modify
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| 25 | % it under the terms of the GNU General Public License as published
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| 26 | % by the Free Software Foundation; either version 2 of the license,
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| 27 | % or (at your option) any later version.
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| 28 | %
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| 29 | % UVMAT is distributed in the hope that it will be useful,
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| 30 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 31 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 32 | % GNU General Public License (see LICENSE.txt) for more details.
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| 33 | %=======================================================================
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| 34 |
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[560] | 35 | function [s,errormsg]=imadoc2struct(ImaDoc,varargin)
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[156] | 36 | %% default input and output
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[565] | 37 | errormsg='';%default
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| 38 | s=[];
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| 39 | % s.Heading=[];%default
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| 40 | % s.Time=[]; %default
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| 41 | % s.TimeUnit=[]; %default
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| 42 | % s.GeometryCalib=[];
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[560] | 43 | % tsai=[];%default
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[8] | 44 |
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[156] | 45 | %% opening the xml file
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[456] | 46 | [tild,tild,FileExt]=fileparts(ImaDoc);
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[560] | 47 | %% case of .civ files (obsolete)
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[456] | 48 | if strcmp(FileExt,'.civ')
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[460] | 49 | [errormsg,time,TimeUnit,mode,npx,npy,s.GeometryCalib]=read_imatext(ImaDoc);
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[456] | 50 | return
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| 51 | end
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[560] | 52 |
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| 53 | %% case of xml files
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[565] | 54 | if nargin ==1
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[685] | 55 | [s,Heading,errormsg]=xml2struct(ImaDoc);% convert the whole xml file in a structure s
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[565] | 56 | elseif nargin ==2
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[685] | 57 | [s,Heading,errormsg]=xml2struct(ImaDoc,varargin{1});% convert the xml file in a structure s, keeping only the subtree defined in input
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[565] | 58 | else %TODO: deal with more than two subtrees?
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[685] | 59 | [s,Heading,errormsg]=xml2struct(ImaDoc,varargin{1},varargin{2});% convert the xml file in a structure s, keeping only the subtree defined in input
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[560] | 60 | end
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[685] | 61 | if ~isempty(errormsg)
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[687] | 62 | errormsg=['error in reading ImaDoc xml file: ' errormsg];
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[685] | 63 | return
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| 64 | end
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[560] | 65 | if ~strcmp(Heading,'ImaDoc')
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[685] | 66 | errormsg='imadoc2struct/the input xml file is not ImaDoc';
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[8] | 67 | return
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| 68 | end
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[560] | 69 | %% reading timing
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[565] | 70 | if isfield(s,'Camera')
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[675] | 71 | if isfield(s.Camera,'TimeUnit')
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| 72 | s.TimeUnit=s.Camera.TimeUnit;
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| 73 | end
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[565] | 74 | Timing=s.Camera.BurstTiming;
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| 75 | if ~iscell(Timing)
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| 76 | Timing={Timing};
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[8] | 77 | end
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[565] | 78 | s.Time=[];
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| 79 | for k=1:length(Timing)
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| 80 | Frequency=1;
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[582] | 81 | if isfield(Timing{k},'FrameFrequency')
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[565] | 82 | Frequency=Timing{k}.FrameFrequency;
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[8] | 83 | end
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[565] | 84 | Dtj=[];
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| 85 | if isfield(Timing{k},'Dtj')
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| 86 | Dtj=Timing{k}.Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's');
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| 87 | end
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| 88 | NbDtj=1;
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| 89 | if isfield(Timing{k},'NbDtj')&&~isempty(Timing{k}.NbDtj)
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| 90 | NbDtj=Timing{k}.NbDtj;
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| 91 | end
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| 92 | Dti=[];
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| 93 | if isfield(Timing{k},'Dti')
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| 94 | Dti=Timing{k}.Dti/Frequency;%Dti converted from frame unit to TimeUnit (e.g. 's');
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| 95 | end
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| 96 | NbDti=1;
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| 97 | if isfield(Timing{k},'NbDti')&&~isempty(Timing{k}.NbDti)
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| 98 | NbDti=Timing{k}.NbDti;
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| 99 | end
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| 100 | Time_val=Timing{k}.Time;%time in TimeUnit
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| 101 | if ~isempty(Dti)
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| 102 | Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
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| 103 | Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals Dti
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| 104 | end
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| 105 | if ~isempty(Dtj)
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| 106 | Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
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| 107 | Dtj=[0 Dtj];
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| 108 | Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
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| 109 | end
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| 110 | % reading Dtk
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| 111 | Dtk=[];%default
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| 112 | NbDtk=1;%default
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[591] | 113 | if isfield(Timing{k},'Dtk')
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[565] | 114 | Dtk=Timing{k}.Dtk;
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| 115 | end
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[591] | 116 | if isfield(Timing{k},'NbDtk')&&~isempty(Timing{k}.NbDtk)
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[565] | 117 | NbDtk=Timing{k}.NbDtk;
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| 118 | end
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| 119 | if isempty(Dtk)
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| 120 | s.Time=[s.Time;Time_val];
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| 121 | else
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| 122 | for kblock=1:NbDtk+1
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| 123 | Time_val_k=Time_val+(kblock-1)*Dtk;
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| 124 | s.Time=[s.Time;Time_val_k];
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| 125 | end
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| 126 | end
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[8] | 127 | end
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[950] | 128 | if ~isfield(s.Camera,'FirstFrameIndexI')
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| 129 | s.Camera.FirstFrameIndexI=1; %first index qssumed equl to 1 by default
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| 130 | end
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[611] | 131 | s.Time=[zeros(size(s.Time,1),1) s.Time]; %insert a vertical line of zeros (to deal with zero file indices)
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[950] | 132 | if s.Camera.FirstFrameIndexI~=0
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| 133 | s.Time=[zeros(s.Camera.FirstFrameIndexI,size(s.Time,2)); s.Time]; %insert a horizontal line of zeros
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| 134 | end
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[8] | 135 | end
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| 136 |
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[191] | 137 | function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
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| 138 | %--------------------------------------------------
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| 139 | s=[];%default
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| 140 | errormsg='';
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[207] | 141 | head_element=get(subt,1,'name');
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[191] | 142 | cont=get(subt,1,'contents');
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| 143 | if ~isempty(cont)
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| 144 | for ilist=1:length(Data)
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[207] | 145 | uid_key=find(subt,[head_element '/' Data{ilist}]);
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[191] | 146 | if ~isequal(length(uid_key),NbOccur(ilist))
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[207] | 147 | errormsg=['wrong number of occurence for ' Data{ilist}];
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[191] | 148 | return
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| 149 | end
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| 150 | for ival=1:length(uid_key)
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[207] | 151 | val=get(subt,children(subt,uid_key(ival)),'value');
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[191] | 152 | if ~NumTest(ilist)
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| 153 | eval(['s.' Data{ilist} '=val;']);
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| 154 | else
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| 155 | eval(['s.' Data{ilist} '=str2double(val);'])
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| 156 | end
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| 157 | end
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| 158 | end
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| 159 | end
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| 160 |
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| 161 |
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| 162 | %--------------------------------------------------
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[8] | 163 | % read an xml element
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| 164 | function val=get_value(t,label,default)
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| 165 | %--------------------------------------------------
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| 166 | val=default;
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| 167 | uid=find(t,label);%find the element iud(s)
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[116] | 168 | if ~isempty(uid) %if the element named label exists
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| 169 | uid_child=children(t,uid);%find the children
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[8] | 170 | if ~isempty(uid_child)
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[116] | 171 | data=get(t,uid_child,'type');%get the type of child
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| 172 | if iscell(data)% case of multiple element
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[8] | 173 | for icell=1:numel(data)
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| 174 | val_read=str2num(get(t,uid_child(icell),'value'));
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| 175 | if ~isempty(val_read)
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[109] | 176 | val(icell,:)=val_read;
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[8] | 177 | end
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| 178 | end
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[116] | 179 | % val=val';
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| 180 | else % case of unique element value
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[8] | 181 | val_read=str2num(get(t,uid_child,'value'));
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| 182 | if ~isempty(val_read)
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| 183 | val=val_read;
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[207] | 184 | else
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| 185 | val=get(t,uid_child,'value');%char string data
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[8] | 186 | end
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| 187 | end
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| 188 | end
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| 189 | end
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[456] | 190 |
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| 191 | %------------------------------------------------------------------------
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| 192 | %'read_imatext': reads the .civ file for image documentation (obsolete)
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| 193 | % fileinput: name of the documentation file
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| 194 | % time: matrix of times for the set of images
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| 195 | %pxcmx: scale along x in pixels/cm
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| 196 | %pxcmy: scale along y in pixels/cm
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| 197 | function [error,time,TimeUnit,mode,npx,npy,GeometryCalib]=read_imatext(fileinput)
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| 198 | %------------------------------------------------------------------------
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[460] | 199 | error='';%default
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[456] | 200 | time=[]; %default
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| 201 | TimeUnit='s';
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| 202 | mode='pairs';
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| 203 | npx=[]; %default
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| 204 | npy=[]; %default
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[460] | 205 | GeometryCalib=[];
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| 206 | if ~exist(fileinput,'file'), error=['image doc file ' fileinput ' does not exist']; return;end;%input file does not exist
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[456] | 207 | dotciv=textread(fileinput);
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| 208 | sizdot=size(dotciv);
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| 209 | if ~isequal(sizdot(1)-8,dotciv(1,1));
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| 210 | error=1; %inconsistent number of bursts
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| 211 | end
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| 212 | nbfield=sizdot(1)-8;
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| 213 | npx=(dotciv(2,1));
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| 214 | npy=(dotciv(2,2));
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| 215 | pxcmx=(dotciv(6,1));% pixels/cm in the .civ file
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| 216 | pxcmy=(dotciv(6,2));
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| 217 | % nburst=dotciv(3,1); % nbre of bursts
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| 218 | abs_time1=dotciv([9:nbfield+8],2);
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| 219 | dtime=dotciv(5,1)*(dotciv([9:nbfield+8],[3:end-1])+1);
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| 220 | timeshift=[abs_time1 dtime];
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| 221 | time=cumsum(timeshift,2);
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[559] | 222 | GeometryCalib.CalibrationType='rescale';
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[456] | 223 | GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
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| 224 | GeometryCalib.Tx=0;
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| 225 | GeometryCalib.Ty=0;
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| 226 | GeometryCalib.Tz=1;
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| 227 | GeometryCalib.dpx=1;
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| 228 | GeometryCalib.dpy=1;
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| 229 | GeometryCalib.sx=1;
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| 230 | GeometryCalib.Cx=0;
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| 231 | GeometryCalib.Cy=0;
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| 232 | GeometryCalib.f=1;
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| 233 | GeometryCalib.kappa1=0;
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[809] | 234 | GeometryCalib.CoordUnit='cm';
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