source: trunk/src/imadoc2struct.m @ 798

%'imadoc2struct': reads the xml file for image documentation 
%------------------------------------------------------------------------
% function [s,errormsg]=imadoc2struct(ImaDoc,option) 
%
% OUTPUT:
% s: structure representing ImaDoc
%   s.Heading: information about the data hierarchical structure
%   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)
%   s.TimeUnit
%  s.GeometryCalib: substructure containing the parameters for geometric calibration
% errormsg: error message
%
% INPUT:
% ImaDoc: full name of the xml input file with head key ImaDoc
% varargin: optional list of strings to restrict the reading to a selection of subtrees, for instance 'GeometryCalib' (save time) 

function [s,errormsg]=imadoc2struct(ImaDoc,varargin) 
%% default input and output
errormsg='';%default
s=[];
% s.Heading=[];%default
% s.Time=[]; %default
% s.TimeUnit=[]; %default
% s.GeometryCalib=[];
% tsai=[];%default

%% opening the xml file
[tild,tild,FileExt]=fileparts(ImaDoc);
%% case of .civ files (obsolete)
if strcmp(FileExt,'.civ')
    [errormsg,time,TimeUnit,mode,npx,npy,s.GeometryCalib]=read_imatext(ImaDoc);
    return
end

%% case of xml files
if nargin ==1
    [s,Heading,errormsg]=xml2struct(ImaDoc);% convert the whole xml file in a structure s
elseif nargin ==2
    [s,Heading,errormsg]=xml2struct(ImaDoc,varargin{1});% convert the xml file in a structure s, keeping only the subtree defined in input
else %TODO: deal with more than two subtrees?
    [s,Heading,errormsg]=xml2struct(ImaDoc,varargin{1},varargin{2});% convert the xml file in a structure s, keeping only the subtree defined in input
end
if ~isempty(errormsg)
    errormsg=['error in reading ImaDoc xml file: ' errormsg];
    return
end
if ~strcmp(Heading,'ImaDoc')
    errormsg='imadoc2struct/the input xml file is not ImaDoc';
    return
end
%% reading timing
if isfield(s,'Camera')
    if isfield(s.Camera,'TimeUnit')
        s.TimeUnit=s.Camera.TimeUnit;
    end
    Timing=s.Camera.BurstTiming;
    if ~iscell(Timing)
        Timing={Timing};
    end
    s.Time=[];
    for k=1:length(Timing)
        Frequency=1;
        if isfield(Timing{k},'FrameFrequency')
            Frequency=Timing{k}.FrameFrequency;
        end
        Dtj=[];
        if isfield(Timing{k},'Dtj')
            Dtj=Timing{k}.Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's');
        end
        NbDtj=1;
        if isfield(Timing{k},'NbDtj')&&~isempty(Timing{k}.NbDtj)
            NbDtj=Timing{k}.NbDtj;
        end
        Dti=[];
        if isfield(Timing{k},'Dti')
            Dti=Timing{k}.Dti/Frequency;%Dti converted from frame unit to TimeUnit (e.g. 's');
        end
        NbDti=1;
        if isfield(Timing{k},'NbDti')&&~isempty(Timing{k}.NbDti)
            NbDti=Timing{k}.NbDti;
        end
        Time_val=Timing{k}.Time;%time in TimeUnit
        if ~isempty(Dti)
            Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
            Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals  Dti
        end
        if ~isempty(Dtj)
            Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
            Dtj=[0 Dtj];
            Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
        end
        % reading Dtk
        Dtk=[];%default
        NbDtk=1;%default
        if isfield(Timing{k},'Dtk')
            Dtk=Timing{k}.Dtk;
        end
        if isfield(Timing{k},'NbDtk')&&~isempty(Timing{k}.NbDtk)
            NbDtk=Timing{k}.NbDtk;
        end
        if isempty(Dtk)
            s.Time=[s.Time;Time_val];
        else
            for kblock=1:NbDtk+1
                Time_val_k=Time_val+(kblock-1)*Dtk;
                s.Time=[s.Time;Time_val_k];
            end
        end
    end
    s.Time=[zeros(size(s.Time,1),1) s.Time]; %insert a vertical line of zeros (to deal with zero file indices)
    s.Time=[zeros(1,size(s.Time,2)); s.Time]; %insert a horizontal line of zeros
end

function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
%--------------------------------------------------
s=[];%default
errormsg='';
head_element=get(subt,1,'name');
    cont=get(subt,1,'contents');
    if ~isempty(cont)
        for ilist=1:length(Data)
            uid_key=find(subt,[head_element '/' Data{ilist}]);
            if ~isequal(length(uid_key),NbOccur(ilist))
                errormsg=['wrong number of occurence for ' Data{ilist}];
                return
            end
            for ival=1:length(uid_key)
                val=get(subt,children(subt,uid_key(ival)),'value');
                if ~NumTest(ilist)
                    eval(['s.' Data{ilist} '=val;']);
                else
                    eval(['s.' Data{ilist} '=str2double(val);'])
                end
            end
        end
    end


%--------------------------------------------------
%  read an xml element
function val=get_value(t,label,default)
%--------------------------------------------------
val=default;
uid=find(t,label);%find the element iud(s)
if ~isempty(uid) %if the element named label exists
   uid_child=children(t,uid);%find the children 
   if ~isempty(uid_child)
       data=get(t,uid_child,'type');%get the type of child
       if iscell(data)% case of multiple element
           for icell=1:numel(data)
               val_read=str2num(get(t,uid_child(icell),'value'));
               if ~isempty(val_read)
                   val(icell,:)=val_read;
               end
           end
%           val=val';
       else % case of unique element value
           val_read=str2num(get(t,uid_child,'value'));
           if ~isempty(val_read)
               val=val_read;
           else
              val=get(t,uid_child,'value');%char string data
           end
       end
   end
end

%------------------------------------------------------------------------
%'read_imatext': reads the .civ file for image documentation (obsolete)
% fileinput: name of the documentation file 
% time: matrix of times for the set of images
%pxcmx: scale along x in pixels/cm
%pxcmy: scale along y in pixels/cm
function [error,time,TimeUnit,mode,npx,npy,GeometryCalib]=read_imatext(fileinput)
%------------------------------------------------------------------------
error='';%default
time=[]; %default
TimeUnit='s';
mode='pairs';
npx=[]; %default
npy=[]; %default
GeometryCalib=[];
if ~exist(fileinput,'file'), error=['image doc file ' fileinput ' does not exist']; return;end;%input file does not exist
dotciv=textread(fileinput);
sizdot=size(dotciv);
if ~isequal(sizdot(1)-8,dotciv(1,1));
    error=1; %inconsistent number of bursts
end
nbfield=sizdot(1)-8;
npx=(dotciv(2,1));
npy=(dotciv(2,2));
pxcmx=(dotciv(6,1));% pixels/cm in the .civ file 
pxcmy=(dotciv(6,2));
% nburst=dotciv(3,1); % nbre of bursts
abs_time1=dotciv([9:nbfield+8],2);
dtime=dotciv(5,1)*(dotciv([9:nbfield+8],[3:end-1])+1);
timeshift=[abs_time1 dtime];
time=cumsum(timeshift,2);
GeometryCalib.CalibrationType='rescale';
GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
GeometryCalib.Tx=0;
GeometryCalib.Ty=0;
GeometryCalib.Tz=1;
GeometryCalib.dpx=1;
GeometryCalib.dpy=1;
GeometryCalib.sx=1;
GeometryCalib.Cx=0;
GeometryCalib.Cy=0;
GeometryCalib.f=1;
GeometryCalib.kappa1=0;
GeometryCalib.CoordUnit='cm';