source: trunk/src/imadoc2struct.m @ 589

Last change on this file since 589 was 582, checked in by sommeria, 8 years ago

various bugs corrected

File size: 16.3 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
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
17function [s,errormsg]=imadoc2struct(ImaDoc,varargin)
18%% default input and output
19errormsg='';%default
20s=[];
21% s.Heading=[];%default
22% s.Time=[]; %default
23% s.TimeUnit=[]; %default
24% s.GeometryCalib=[];
25% tsai=[];%default
26
27%% opening the xml file
28[tild,tild,FileExt]=fileparts(ImaDoc);
29%% case of .civ files (obsolete)
30if strcmp(FileExt,'.civ')
31    [errormsg,time,TimeUnit,mode,npx,npy,s.GeometryCalib]=read_imatext(ImaDoc);
32    return
33end
34
35%% case of xml files
36if nargin ==1
37    [s,Heading]=xml2struct(ImaDoc);% convert the whole xml file in a structure s
38elseif nargin ==2
39    [s,Heading]=xml2struct(ImaDoc,varargin{1});% convert the xml file in a structure s, keeping only the subtree defined in input
40else %TODO: deal with more than two subtrees?
41    [s,Heading]=xml2struct(ImaDoc,varargin{1},varargin{2});% convert the xml file in a structure s, keeping only the subtree defined in input
42end
43if ~strcmp(Heading,'ImaDoc')
44    errormsg='the input xml file is not ImaDoc';
45    return
46end
47%% reading timing
48if isfield(s,'Camera')
49    Timing=s.Camera.BurstTiming;
50    if ~iscell(Timing)
51        Timing={Timing};
52    end
53    s.Time=[];
54    for k=1:length(Timing)
55        Frequency=1;
56        if isfield(Timing{k},'FrameFrequency')
57            Frequency=Timing{k}.FrameFrequency;
58        end
59        Dtj=[];
60        if isfield(Timing{k},'Dtj')
61            Dtj=Timing{k}.Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's');
62        end
63        NbDtj=1;
64        if isfield(Timing{k},'NbDtj')&&~isempty(Timing{k}.NbDtj)
65            NbDtj=Timing{k}.NbDtj;
66        end
67        Dti=[];
68        if isfield(Timing{k},'Dti')
69            Dti=Timing{k}.Dti/Frequency;%Dti converted from frame unit to TimeUnit (e.g. 's');
70        end
71        NbDti=1;
72        if isfield(Timing{k},'NbDti')&&~isempty(Timing{k}.NbDti)
73            NbDti=Timing{k}.NbDti;
74        end
75        Time_val=Timing{k}.Time;%time in TimeUnit
76        if ~isempty(Dti)
77            Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
78            Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals  Dti
79        end
80        if ~isempty(Dtj)
81            Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
82            Dtj=[0 Dtj];
83            Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
84        end
85        % reading Dtk
86        Dtk=[];%default
87        NbDtk=1;%default
88        if isfield(Timing,'Dtk')
89            Dtk=Timing{k}.Dtk;
90        end
91        if isfield(Timing,'NbDtk')&&~isempty(Timing{k}.NbDtk)
92            NbDtk=Timing{k}.NbDtk;
93        end
94        if isempty(Dtk)
95            s.Time=[s.Time;Time_val];
96        else
97            for kblock=1:NbDtk+1
98                Time_val_k=Time_val+(kblock-1)*Dtk;
99                s.Time=[s.Time;Time_val_k];
100            end
101        end
102    end
103end
104
105% try
106%     t=xmltree(ImaDoc);
107% catch ME
108%     errormsg={['error reading ' ImaDoc ': ']; ME.message};
109%     display(errormsg);
110%     return
111% end
112% uid_root=find(t,'/ImaDoc');
113% if isempty(uid_root), return; end;%not an ImaDoc .xml file
114
115% %% Heading
116% uid_Heading=find(t,'/ImaDoc/Heading');
117% if ~isempty(uid_Heading),
118%     uid_Campaign=find(t,'/ImaDoc/Heading/Campaign');
119%     uid_Exp=find(t,'/ImaDoc/Heading/Experiment');
120%     uid_Device=find(t,'/ImaDoc/Heading/Device');
121%     uid_Record=find(t,'/ImaDoc/Heading/Record');
122%     uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName');
123%     s.Heading.Campaign=get(t,children(t,uid_Campaign),'value');
124%     s.Heading.Experiment=get(t,children(t,uid_Exp),'value');
125%     s.Heading.Device=get(t,children(t,uid_Device),'value');
126%     if ~isempty(uid_Record)
127%         s.Heading.Record=get(t,children(t,uid_Record),'value');
128%     end
129%     s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value');
130% end
131
132%% Camera  and timing
133% if strcmp(option,'*') || strcmp(option,'Camera')
134%     uid_Camera=find(t,'/ImaDoc/Camera');
135%     if ~isempty(uid_Camera)
136%         uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize');
137%         if ~isempty(uid_ImageSize);
138%             ImageSize=get(t,children(t,uid_ImageSize),'value');
139%             xindex=findstr(ImageSize,'x');
140%             if length(xindex)>=2
141%                 s.Npx=str2double(ImageSize(1:xindex(1)-1));
142%                 s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1));
143%             end
144%         end
145%         uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit');
146%         if ~isempty(uid_TimeUnit)
147%             s.TimeUnit=get(t,children(t,uid_TimeUnit),'value');
148%         end
149%         uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming');
150%         if ~isempty(uid_BurstTiming)
151%             for k=1:length(uid_BurstTiming)
152%                 subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming
153%                 % reading Dtk
154%                 Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1);
155%                 Dtj=get_value(subt,'/BurstTiming/Dtj',[]);
156%                 Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
157%                 NbDtj=get_value(subt,'/BurstTiming/NbDtj',1);
158%                 Dti=get_value(subt,'/BurstTiming/Dti',[]);
159%                 Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
160%                 NbDti=get_value(subt,'/BurstTiming/NbDti',1);
161%                 Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit
162%                 if ~isempty(Dti)
163%                     Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
164%                     Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals  Dti
165%                 end
166%                 if ~isempty(Dtj)
167%                     Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
168%                     Dtj=[0 Dtj];
169%                     Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
170%                 end
171%                 % reading Dtk
172%                 Dtk=get_value(subt,'/BurstTiming/Dtk',[]);
173%                 NbDtk=get_value(subt,'/BurstTiming/NbDtk',1);
174%                 if isempty(Dtk)
175%                     s.Time=[s.Time;Time_val];
176%                 else
177%                     for kblock=1:NbDtk+1
178%                         Time_val_k=Time_val+(kblock-1)*Dtk;
179%                         s.Time=[s.Time;Time_val_k];
180%                     end
181%                 end
182%             end
183%         end
184%     end
185% end
186
187%% motor
188% if strcmp(option,'*') || strcmp(option,'GeometryCalib')
189%     uid_subtree=find(t,'/ImaDoc/TranslationMotor');
190%     if length(uid_subtree)==1
191%         subt=branch(t,uid_subtree);%subtree under GeometryCalib
192%        [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]);
193%     end
194% end
195%%  geometric calibration
196% if strcmp(option,'*') || strcmp(option,'GeometryCalib')
197%     uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib');
198%     if ~isempty(uid_GeometryCalib)
199%         if length(uid_GeometryCalib)>1
200%             errormsg=['More than one GeometryCalib in ' filecivxml];
201%             return
202%         end
203%         subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib
204%         cont=get(subt,1,'contents');
205%         if ~isempty(cont)
206%             uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType');
207%             if isequal(length(uid_CalibrationType),1)
208%                 tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value');
209%             end
210%             uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit');
211%             if isequal(length(uid_CoordUnit),1)
212%                 tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value');
213%             end
214%             uid_fx_fy=find(subt,'/GeometryCalib/fx_fy');
215%             focal=[];%default fro old convention (Reg Wilson)
216%             if isequal(length(uid_fx_fy),1)
217%                 tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value'));
218%             else %old convention (Reg Wilson)
219%                 uid_focal=find(subt,'/GeometryCalib/focal');
220%                 uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy');
221%                 uid_sx=find(subt,'/GeometryCalib/sx');
222%                 if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx)
223%                     dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value'));
224%                     sx=str2num(get(subt,children(subt,uid_sx),'value'));
225%                     focal=str2num(get(subt,children(subt,uid_focal),'value'));
226%                     tsai.fx_fy(1)=sx*focal/dpx_dpy(1);
227%                     tsai.fx_fy(2)=focal/dpx_dpy(2);
228%                 end
229%             end
230%             uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy');
231%             if ~isempty(uid_Cx_Cy)
232%                 tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value'));
233%             end
234%             uid_kc=find(subt,'/GeometryCalib/kc');
235%             if ~isempty(uid_kc)
236%                 tsai.kc=str2double(get(subt,children(subt,uid_kc),'value'));
237%             else %old convention (Reg Wilson)
238%                 uid_kappa1=find(subt,'/GeometryCalib/kappa1');
239%                 if ~isempty(uid_kappa1)&& ~isempty(focal)
240%                     kappa1=str2double(get(subt,children(subt,uid_kappa1),'value'));
241%                     tsai.kc=-kappa1*focal*focal;
242%                 end
243%             end
244%             uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz');
245%             if ~isempty(uid_Tx_Ty_Tz)
246%                 tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value'));
247%             end
248%             uid_R=find(subt,'/GeometryCalib/R');
249%             if ~isempty(uid_R)
250%                 RR=get(subt,children(subt,uid_R),'value');
251%                 if length(RR)==3
252%                     tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})];
253%                 end
254%             end
255%             
256%             %look for laser plane definitions
257%             uid_Angle=find(subt,'/GeometryCalib/PlaneAngle');
258%             uid_Pos=find(subt,'/GeometryCalib/SliceCoord');
259%             if isempty(uid_Pos)
260%                 uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention
261%             end
262%             if ~isempty(uid_Angle)
263%                 tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value'));
264%             end
265%             if ~isempty(uid_Pos)
266%                 for j=1:length(uid_Pos)
267%                     tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value'));
268%                 end
269%                 uid_DZ=find(subt,'/GeometryCalib/SliceDZ');
270%                 uid_NbSlice=find(subt,'/GeometryCalib/NbSlice');
271%                 if ~isempty(uid_DZ) && ~isempty(uid_NbSlice)
272%                     DZ=str2double(get(subt,children(subt,uid_DZ),'value'));
273%                     NbSlice=get(subt,children(subt,uid_NbSlice),'value');
274%                     if isequal(NbSlice,'volume')
275%                         tsai.NbSlice='volume';
276%                         NbSlice=NbDtj+1;
277%                     else
278%                         tsai.NbSlice=str2double(NbSlice);
279%                     end
280%                     tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1];
281%                 end
282%             end   
283%             tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]);
284%             tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n');
285%             tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]);
286%             tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1);
287%             
288%             if strcmp(option,'GeometryCalib')
289%                 tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]);
290%             end
291%             s.GeometryCalib=tsai;
292%         end
293%     end
294% end
295
296%--------------------------------------------------
297%  read a subtree
298% INPUT:
299% t: xltree
300% head_element: head elelemnt of the subtree
301% Data, structure containing
302%    .Key: element name
303%    .Type: type of element ('charg', 'float'....)
304%    .NbOccur: nbre of occurrence, NaN for un specified number
305function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
306%--------------------------------------------------
307s=[];%default
308errormsg='';
309head_element=get(subt,1,'name');
310    cont=get(subt,1,'contents');
311    if ~isempty(cont)
312        for ilist=1:length(Data)
313            uid_key=find(subt,[head_element '/' Data{ilist}]);
314            if ~isequal(length(uid_key),NbOccur(ilist))
315                errormsg=['wrong number of occurence for ' Data{ilist}];
316                return
317            end
318            for ival=1:length(uid_key)
319                val=get(subt,children(subt,uid_key(ival)),'value');
320                if ~NumTest(ilist)
321                    eval(['s.' Data{ilist} '=val;']);
322                else
323                    eval(['s.' Data{ilist} '=str2double(val);'])
324                end
325            end
326        end
327    end
328
329
330%--------------------------------------------------
331%  read an xml element
332function val=get_value(t,label,default)
333%--------------------------------------------------
334val=default;
335uid=find(t,label);%find the element iud(s)
336if ~isempty(uid) %if the element named label exists
337   uid_child=children(t,uid);%find the children
338   if ~isempty(uid_child)
339       data=get(t,uid_child,'type');%get the type of child
340       if iscell(data)% case of multiple element
341           for icell=1:numel(data)
342               val_read=str2num(get(t,uid_child(icell),'value'));
343               if ~isempty(val_read)
344                   val(icell,:)=val_read;
345               end
346           end
347%           val=val';
348       else % case of unique element value
349           val_read=str2num(get(t,uid_child,'value'));
350           if ~isempty(val_read)
351               val=val_read;
352           else
353              val=get(t,uid_child,'value');%char string data
354           end
355       end
356   end
357end
358
359%------------------------------------------------------------------------
360%'read_imatext': reads the .civ file for image documentation (obsolete)
361% fileinput: name of the documentation file
362% time: matrix of times for the set of images
363%pxcmx: scale along x in pixels/cm
364%pxcmy: scale along y in pixels/cm
365function [error,time,TimeUnit,mode,npx,npy,GeometryCalib]=read_imatext(fileinput)
366%------------------------------------------------------------------------
367error='';%default
368time=[]; %default
369TimeUnit='s';
370mode='pairs';
371npx=[]; %default
372npy=[]; %default
373GeometryCalib=[];
374if ~exist(fileinput,'file'), error=['image doc file ' fileinput ' does not exist']; return;end;%input file does not exist
375dotciv=textread(fileinput);
376sizdot=size(dotciv);
377if ~isequal(sizdot(1)-8,dotciv(1,1));
378    error=1; %inconsistent number of bursts
379end
380nbfield=sizdot(1)-8;
381npx=(dotciv(2,1));
382npy=(dotciv(2,2));
383pxcmx=(dotciv(6,1));% pixels/cm in the .civ file
384pxcmy=(dotciv(6,2));
385% nburst=dotciv(3,1); % nbre of bursts
386abs_time1=dotciv([9:nbfield+8],2);
387dtime=dotciv(5,1)*(dotciv([9:nbfield+8],[3:end-1])+1);
388timeshift=[abs_time1 dtime];
389time=cumsum(timeshift,2);
390GeometryCalib.CalibrationType='rescale';
391GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
392GeometryCalib.Tx=0;
393GeometryCalib.Ty=0;
394GeometryCalib.Tz=1;
395GeometryCalib.dpx=1;
396GeometryCalib.dpy=1;
397GeometryCalib.sx=1;
398GeometryCalib.Cx=0;
399GeometryCalib.Cy=0;
400GeometryCalib.f=1;
401GeometryCalib.kappa1=0;
402GeometryCalib.CoordUnit='cm';
Note: See TracBrowser for help on using the repository browser.