source: trunk/src/imadoc2struct.m @ 1149

Last change on this file since 1149 was 1149, checked in by sommeria, 3 months ago

extract_rdvision improved by automatic production of the xml file from timestamps

File size: 8.4 KB
Line 
1%'imadoc2struct': reads the xml file for image documentation
2%------------------------------------------------------------------------
3% function [s,errormsg]=imadoc2struct(ImaDoc,option)
4%
5% OUTPUT:
6% s: structure representing ImaDoc
7%   s.Heading: information about the data hierarchical structure
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)
9%   s.TimeUnit
10%  s.GeometryCalib: substructure containing the parameters for geometric calibration
11% errormsg: error message
12%
13% INPUT:
14% ImaDoc: full name of the xml input file with head key ImaDoc
15% varargin: optional list of strings to restrict the reading to a selection of subtrees, for instance 'GeometryCalib' (save time)
16
17%=======================================================================
18% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
19%   http://www.legi.grenoble-inp.fr
20%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
21%
22%     This file is part of the toolbox UVMAT.
23%
24%     UVMAT is free software; you can redistribute it and/or modify
25%     it under the terms of the GNU General Public License as published
26%     by the Free Software Foundation; either version 2 of the license,
27%     or (at your option) any later version.
28%
29%     UVMAT is distributed in the hope that it will be useful,
30%     but WITHOUT ANY WARRANTY; without even the implied warranty of
31%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
32%     GNU General Public License (see LICENSE.txt) for more details.
33%=======================================================================
34
35function [s,errormsg]=imadoc2struct(ImaDoc,varargin)
36%% default input and output
37errormsg='';%default
38s=[];
39
40%% opening the xml file
41[tild,tild,FileExt]=fileparts(ImaDoc);
42%% case of .civ files (obsolete)
43if strcmp(FileExt,'.civ')
44    [errormsg,time,TimeUnit,mode,npx,npy,s.GeometryCalib]=read_imatext(ImaDoc);
45    return
46end
47
48%% case of xml files
49if nargin ==1
50    [s,Heading,errormsg]=xml2struct(ImaDoc);% convert the whole xml file in a structure s
51elseif nargin ==2
52    [s,Heading,errormsg]=xml2struct(ImaDoc,varargin{1});% convert the xml file in a structure s, keeping only the subtree defined in input
53else %TODO: deal with more than two subtrees?
54    [s,Heading,errormsg]=xml2struct(ImaDoc,varargin{1},varargin{2});% convert the xml file in a structure s, keeping only the subtree defined in input
55end
56if ~isempty(errormsg)
57    errormsg=['error in reading ImaDoc xml file: ' errormsg];
58    return
59end
60if ~strcmp(Heading,'ImaDoc')
61    errormsg='imadoc2struct/the input xml file is not ImaDoc';
62    return
63end
64%% reading timing
65if isfield(s,'Camera')
66    if isfield(s.Camera,'TimeUnit')
67        s.TimeUnit=s.Camera.TimeUnit;
68    end
69    if ~isfield(s.Camera,'FirstFrameIndexI')
70        s.Camera.FirstFrameIndexI=1; %first index assumed equl to 1 by default
71    end
72    Timing=s.Camera.BurstTiming;
73    if ~iscell(Timing)
74        Timing={Timing};
75    end
76
77    s.Time=[];
78    for k=1:length(Timing)
79        Frequency=1;
80        if isfield(Timing{k},'FrameFrequency')
81            Frequency=Timing{k}.FrameFrequency;
82        end
83        Dtj=[];
84        if isfield(Timing{k},'Dtj')
85            Dtj=Timing{k}.Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's');
86        end
87        NbDtj=1;
88        if isfield(Timing{k},'NbDtj')&&~isempty(Timing{k}.NbDtj)
89            NbDtj=Timing{k}.NbDtj;
90        end
91        Dti=[];
92        if isfield(Timing{k},'Dti')
93            Dti=Timing{k}.Dti/Frequency;%Dti converted from frame unit to TimeUnit (e.g. 's');
94        end
95        NbDti=1;
96        if isfield(Timing{k},'NbDti')&&~isempty(Timing{k}.NbDti)
97            NbDti=Timing{k}.NbDti;
98        end
99        Time_val=Timing{k}.Time;%time in TimeUnit
100        if ~isempty(Dti)
101            Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
102            Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals  Dti
103        end
104        if ~isempty(Dtj)
105            Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
106            Dtj=[0 Dtj];
107            Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
108        end
109        % reading Dtk
110        Dtk=[];%default
111        NbDtk=1;%default
112        if isfield(Timing{k},'Dtk')
113            Dtk=Timing{k}.Dtk;
114        end
115        if isfield(Timing{k},'NbDtk')&&~isempty(Timing{k}.NbDtk)
116            NbDtk=Timing{k}.NbDtk;
117        end
118        if isempty(Dtk)
119            s.Time=[s.Time;Time_val];
120        else
121            for kblock=1:NbDtk+1
122                Time_val_k=Time_val+(kblock-1)*Dtk;
123                s.Time=[s.Time;Time_val_k];
124            end
125        end
126    end
127   
128    s.Time=[zeros(size(s.Time,1),1) s.Time]; %insert a vertical line of zeros (to deal with zero file indices)
129    if s.Camera.FirstFrameIndexI~=0
130    s.Time=[zeros(s.Camera.FirstFrameIndexI,size(s.Time,2)); s.Time]; %insert a horizontal line of zeros
131    end
132end
133
134function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
135%--------------------------------------------------
136s=[];%default
137errormsg='';
138head_element=get(subt,1,'name');
139    cont=get(subt,1,'contents');
140    if ~isempty(cont)
141        for ilist=1:length(Data)
142            uid_key=find(subt,[head_element '/' Data{ilist}]);
143            if ~isequal(length(uid_key),NbOccur(ilist))
144                errormsg=['wrong number of occurence for ' Data{ilist}];
145                return
146            end
147            for ival=1:length(uid_key)
148                val=get(subt,children(subt,uid_key(ival)),'value');
149                if ~NumTest(ilist)
150                    eval(['s.' Data{ilist} '=val;']);
151                else
152                    eval(['s.' Data{ilist} '=str2double(val);'])
153                end
154            end
155        end
156    end
157
158
159%--------------------------------------------------
160%  read an xml element
161function val=get_value(t,label,default)
162%--------------------------------------------------
163val=default;
164uid=find(t,label);%find the element iud(s)
165if ~isempty(uid) %if the element named label exists
166   uid_child=children(t,uid);%find the children
167   if ~isempty(uid_child)
168       data=get(t,uid_child,'type');%get the type of child
169       if iscell(data)% case of multiple element
170           for icell=1:numel(data)
171               val_read=str2num(get(t,uid_child(icell),'value'));
172               if ~isempty(val_read)
173                   val(icell,:)=val_read;
174               end
175           end
176%           val=val';
177       else % case of unique element value
178           val_read=str2num(get(t,uid_child,'value'));
179           if ~isempty(val_read)
180               val=val_read;
181           else
182              val=get(t,uid_child,'value');%char string data
183           end
184       end
185   end
186end
187
188%------------------------------------------------------------------------
189%'read_imatext': reads the .civ file for image documentation (obsolete)
190% fileinput: name of the documentation file
191% time: matrix of times for the set of images
192%pxcmx: scale along x in pixels/cm
193%pxcmy: scale along y in pixels/cm
194function [error,time,TimeUnit,mode,npx,npy,GeometryCalib]=read_imatext(fileinput)
195%------------------------------------------------------------------------
196error='';%default
197time=[]; %default
198TimeUnit='s';
199mode='pairs';
200npx=[]; %default
201npy=[]; %default
202GeometryCalib=[];
203if ~exist(fileinput,'file'), error=['image doc file ' fileinput ' does not exist']; return;end;%input file does not exist
204dotciv=textread(fileinput);
205sizdot=size(dotciv);
206if ~isequal(sizdot(1)-8,dotciv(1,1));
207    error=1; %inconsistent number of bursts
208end
209nbfield=sizdot(1)-8;
210npx=(dotciv(2,1));
211npy=(dotciv(2,2));
212pxcmx=(dotciv(6,1));% pixels/cm in the .civ file
213pxcmy=(dotciv(6,2));
214% nburst=dotciv(3,1); % nbre of bursts
215abs_time1=dotciv([9:nbfield+8],2);
216dtime=dotciv(5,1)*(dotciv([9:nbfield+8],[3:end-1])+1);
217timeshift=[abs_time1 dtime];
218time=cumsum(timeshift,2);
219GeometryCalib.CalibrationType='rescale';
220GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
221GeometryCalib.Tx=0;
222GeometryCalib.Ty=0;
223GeometryCalib.Tz=1;
224GeometryCalib.dpx=1;
225GeometryCalib.dpy=1;
226GeometryCalib.sx=1;
227GeometryCalib.Cx=0;
228GeometryCalib.Cy=0;
229GeometryCalib.f=1;
230GeometryCalib.kappa1=0;
231GeometryCalib.CoordUnit='cm';
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