%'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]=xml2struct(ImaDoc);% convert the whole xml file in a structure s
elseif nargin ==2
    [s,Heading]=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]=xml2struct(ImaDoc,varargin{1},varargin{2});% convert the xml file in a structure s, keeping only the subtree defined in input
end
if ~strcmp(Heading,'ImaDoc')
    errormsg='the input xml file is not ImaDoc';
    return
end
%% reading timing
if isfield(s,'Camera')
    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

% try
%     t=xmltree(ImaDoc);
% catch ME
%     errormsg={['error reading ' ImaDoc ': ']; ME.message};
%     display(errormsg);
%     return
% end
% uid_root=find(t,'/ImaDoc');
% if isempty(uid_root), return; end;%not an ImaDoc .xml file

% %% Heading
% uid_Heading=find(t,'/ImaDoc/Heading');
% if ~isempty(uid_Heading), 
%     uid_Campaign=find(t,'/ImaDoc/Heading/Campaign');
%     uid_Exp=find(t,'/ImaDoc/Heading/Experiment');
%     uid_Device=find(t,'/ImaDoc/Heading/Device');
%     uid_Record=find(t,'/ImaDoc/Heading/Record');
%     uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName');
%     s.Heading.Campaign=get(t,children(t,uid_Campaign),'value');
%     s.Heading.Experiment=get(t,children(t,uid_Exp),'value');
%     s.Heading.Device=get(t,children(t,uid_Device),'value');
%     if ~isempty(uid_Record)
%         s.Heading.Record=get(t,children(t,uid_Record),'value');
%     end
%     s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value');
% end

%% Camera  and timing
% if strcmp(option,'*') || strcmp(option,'Camera')
%     uid_Camera=find(t,'/ImaDoc/Camera');
%     if ~isempty(uid_Camera)
%         uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize');
%         if ~isempty(uid_ImageSize);
%             ImageSize=get(t,children(t,uid_ImageSize),'value');
%             xindex=findstr(ImageSize,'x');
%             if length(xindex)>=2
%                 s.Npx=str2double(ImageSize(1:xindex(1)-1));
%                 s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1));
%             end
%         end
%         uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit');
%         if ~isempty(uid_TimeUnit)
%             s.TimeUnit=get(t,children(t,uid_TimeUnit),'value');
%         end
%         uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming');
%         if ~isempty(uid_BurstTiming)
%             for k=1:length(uid_BurstTiming)
%                 subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming
%                 % reading Dtk
%                 Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1);
%                 Dtj=get_value(subt,'/BurstTiming/Dtj',[]);
%                 Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
%                 NbDtj=get_value(subt,'/BurstTiming/NbDtj',1);
%                 Dti=get_value(subt,'/BurstTiming/Dti',[]);
%                 Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
%                 NbDti=get_value(subt,'/BurstTiming/NbDti',1);
%                 Time_val=get_value(subt,'/BurstTiming/Time',0);%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=get_value(subt,'/BurstTiming/Dtk',[]);
%                 NbDtk=get_value(subt,'/BurstTiming/NbDtk',1);
%                 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
%         end
%     end
% end

%% motor
% if strcmp(option,'*') || strcmp(option,'GeometryCalib')
%     uid_subtree=find(t,'/ImaDoc/TranslationMotor');
%     if length(uid_subtree)==1
%         subt=branch(t,uid_subtree);%subtree under GeometryCalib
%        [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]);
%     end 
% end
%%  geometric calibration
% if strcmp(option,'*') || strcmp(option,'GeometryCalib')
%     uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib');
%     if ~isempty(uid_GeometryCalib)
%         if length(uid_GeometryCalib)>1
%             errormsg=['More than one GeometryCalib in ' filecivxml];
%             return
%         end
%         subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib
%         cont=get(subt,1,'contents');
%         if ~isempty(cont)
%             uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType');
%             if isequal(length(uid_CalibrationType),1)
%                 tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value');
%             end
%             uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit');
%             if isequal(length(uid_CoordUnit),1)
%                 tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value');
%             end
%             uid_fx_fy=find(subt,'/GeometryCalib/fx_fy');
%             focal=[];%default fro old convention (Reg Wilson)
%             if isequal(length(uid_fx_fy),1)
%                 tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value'));
%             else %old convention (Reg Wilson)
%                 uid_focal=find(subt,'/GeometryCalib/focal');
%                 uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy');
%                 uid_sx=find(subt,'/GeometryCalib/sx');
%                 if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx)
%                     dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value'));
%                     sx=str2num(get(subt,children(subt,uid_sx),'value'));
%                     focal=str2num(get(subt,children(subt,uid_focal),'value'));
%                     tsai.fx_fy(1)=sx*focal/dpx_dpy(1);
%                     tsai.fx_fy(2)=focal/dpx_dpy(2);
%                 end
%             end
%             uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy');
%             if ~isempty(uid_Cx_Cy)
%                 tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value'));
%             end
%             uid_kc=find(subt,'/GeometryCalib/kc');
%             if ~isempty(uid_kc)
%                 tsai.kc=str2double(get(subt,children(subt,uid_kc),'value'));
%             else %old convention (Reg Wilson)
%                 uid_kappa1=find(subt,'/GeometryCalib/kappa1');
%                 if ~isempty(uid_kappa1)&& ~isempty(focal)
%                     kappa1=str2double(get(subt,children(subt,uid_kappa1),'value'));
%                     tsai.kc=-kappa1*focal*focal;
%                 end
%             end
%             uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz');
%             if ~isempty(uid_Tx_Ty_Tz)
%                 tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value'));
%             end
%             uid_R=find(subt,'/GeometryCalib/R');
%             if ~isempty(uid_R)
%                 RR=get(subt,children(subt,uid_R),'value');
%                 if length(RR)==3
%                     tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})];
%                 end
%             end
%             
%             %look for laser plane definitions
%             uid_Angle=find(subt,'/GeometryCalib/PlaneAngle');
%             uid_Pos=find(subt,'/GeometryCalib/SliceCoord');
%             if isempty(uid_Pos)
%                 uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention
%             end
%             if ~isempty(uid_Angle)
%                 tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value'));
%             end
%             if ~isempty(uid_Pos)
%                 for j=1:length(uid_Pos)
%                     tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value'));
%                 end
%                 uid_DZ=find(subt,'/GeometryCalib/SliceDZ');
%                 uid_NbSlice=find(subt,'/GeometryCalib/NbSlice');
%                 if ~isempty(uid_DZ) && ~isempty(uid_NbSlice)
%                     DZ=str2double(get(subt,children(subt,uid_DZ),'value'));
%                     NbSlice=get(subt,children(subt,uid_NbSlice),'value');
%                     if isequal(NbSlice,'volume')
%                         tsai.NbSlice='volume';
%                         NbSlice=NbDtj+1;
%                     else
%                         tsai.NbSlice=str2double(NbSlice);
%                     end
%                     tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1];
%                 end
%             end   
%             tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]);
%             tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n');
%             tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]);
%             tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1);
%             
%             if strcmp(option,'GeometryCalib')
%                 tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]);
%             end
%             s.GeometryCalib=tsai;
%         end
%     end
% end

%--------------------------------------------------
%  read a subtree
% INPUT: 
% t: xltree
% head_element: head elelemnt of the subtree
% Data, structure containing 
%    .Key: element name
%    .Type: type of element ('charg', 'float'....)
%    .NbOccur: nbre of occurrence, NaN for un specified number 
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';