%'time_series': extract a time series, used with series.fig
% this function can be used as a template for applying a global operation on a series of input fields
%------------------------------------------------------------------------
% function GUI_input=time_series(Param)
%
%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This function is used in four modes by the GUI series:
%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced. 
%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
%
% This function is used in four modes by the GUI series:
%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced. 
%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
%
%OUTPUT
% GUI_input=list of options in the GUI series.fig needed for the function
%
%INPUT:
% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
% In batch mode, Param is the name of the corresponding xml file containing the same information
% In the absence of input (as activated when the current Action is selected
% in series), the function ouput GUI_input set the activation of the needed GUI elements
%
% Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param)
%    .InputTable: cell of input file names, (several lines for multiple input)
%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
%    .OutputSubDir: name of the subdirectory for data outputs
%    .OutputDirExt: directory extension for data outputs
%    .Action: .ActionName: name of the current activated function
%             .ActionPath:   path of the current activated function
%    .IndexRange: set the file or frame indices on which the action must be performed
%    .FieldTransform: .TransformName: name of the selected transform function
%                     .TransformPath:   path  of the selected transform function
%                     .TransformHandle: corresponding function handle
%    .InputFields: sub structure describing the input fields withfields
%              .FieldName: name of the field
%              .VelType: velocity type
%              .FieldName_1: name of the second field in case of two input series
%              .VelType_1: velocity type of the second field in case of two input series
%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
function ParamOut=time_series(Param) 

%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
if ~exist('Param','var') % case with no input parameter 
    ParamOut={'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default)
        'WholeIndexRange';'off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
        'NbSlice';'on'; ...%nbre of slices ('off' by default)
        'VelType';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
        'FieldName';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
        'FieldTransform'; 'on';...%can use a transform function
        'ProjObject';'on';...%can use projection object(option 'off'/'on',
        'Mask';'off';...%can use mask option   (option 'off'/'on', 'off' by default)
        'OutputDirExt';'.tseries';...%set the output dir extension
               ''};
        return
end

%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
%% select different modes,  RUN, parameter input, BATCH
% BATCH  case: read the xml file for batch case
if ischar(Param)
        Param=xml2struct(Param);
        checkrun=0;
% RUN case: parameters introduced as the input structure Param
else
    hseries=guidata(Param.hseries);%handles of the GUI series
    if isfield(Param,'Specific')&& strcmp(Param.Specific,'?')
        checkrun=1;% will only search interactive input parameters (preparation of BATCH mode)
    else
        checkrun=2; % indicate the RUN option is used
    end
end
ParamOut=Param; %default output
OutputDir=[Param.OutputSubDir Param.OutputDirExt];

%% root input file(s) and type
RootPath=Param.InputTable(:,1);
RootFile=Param.InputTable(:,3);
SubDir=Param.InputTable(:,2);
NomType=Param.InputTable(:,4);
FileExt=Param.InputTable(:,5);

% get the set of input file names (cell array filecell), and the lists of
% input file or frame indices i1_series,i2_series,j1_series,j2_series
[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
% filecell{iview,fileindex}: cell array representing the list of file names
%        iview: line in the table corresponding to a given file series
%        fileindex: file index within  the file series, 
% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j 
% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
% set of frame indices used for movie or multimage input 
% numbers of slices and file indices

NbSlice=1;%default
if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
    NbSlice=Param.IndexRange.NbSlice;
end
nbview=numel(i1_series);%number of input file series (lines in InputTable)
nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
nbfield_i=size(i1_series{1},2); %nb of fields for the i index
nbfield=nbfield_j*nbfield_i; %total number of fields
nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices) 
nbfield=nbfield_i*NbSlice; %total number of fields after adjustement

%determine the file type on each line from the first input file 
ImageTypeOptions={'image','multimage','mmreader','video'};
NcTypeOptions={'netcdf','civx','civdata'};
for iview=1:nbview
    if ~exist(filecell{iview,1}','file')
        displ_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
        return
    end
    [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1});
    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
    if ~isempty(j1_series{iview})
        frame_index{iview}=j1_series{iview};
    else
        frame_index{iview}=i1_series{iview};
    end
end

%% calibration data and timing: read the ImaDoc files
[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
if size(time,1)>1
    diff_time=max(max(diff(time)));
    if diff_time>0
        displ_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
    end   
end

%% coordinate transform or other user defined transform
transform_fct='';%default
if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
    addpath(Param.FieldTransform.TransformPath)
    transform_fct=str2func(Param.FieldTransform.TransformName);
    rmpath(Param.FieldTransform.TransformPath)
end

%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
 % EDIT FROM HERE

%% check the validity of  input file types
if CheckImage{1}
    FileExtOut='.png'; % write result as .png images for image inputs
elseif CheckNc{1}
    FileExtOut='.nc';% write result as .nc files for netcdf inputs
else 
    displ_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
    return
end
if nbview==2 && ~isequal(CheckImage{1},CheckImage{2})
        displ_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
    return
end
NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series
% if NbSlice~=nbfield_j
%     answer=_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]);
%     if ~strcmp(answer,'Yes')
%         return
%     end
% end
if checkrun==1
    return % stop here for input checks
end

%% Set field names and velocity types
InputFields{1}=[];%default (case of images)
if isfield(Param,'InputFields')
    InputFields{1}=Param.InputFields;
end
if nbview==2
    InputFields{2}=[];%default (case of images)
    if isfield(Param,'InputFields')
        InputFields{2}=Param.InputFields{1};%default
        if isfield(Param.InputFields,'FieldName_1')
            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
            if isfield(Param.InputFields,'VelType_1')
                InputFields{2}.VelType=Param.InputFields.VelType_1;
            end
        end
    end
end
%%% TO UPDATE
if isequal(InputFields{1},'get_field...')
    hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
    if numel(hget_field)>1
        delete(hget_field(2:end)) % delete multiple occurerence of the GUI get_fioeld
    elseif isempty(hget_field)
        filename=filecell{1,1};
      % filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),num_j2{1}(1),SubDir{1}); 
       idetect(iview)=exist(filename,'file');
       hget_field=get_field(filename);
       return
    end
    SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
    if isempty(SubField)
        delete(hget_field)
        filename=filecell{1,1};
       %filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),j2_series{1}(1),SubDir{1});
        hget_field=get_field(filename);
        SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
    end
end
%%%%%%%

%% Initiate output fields
%initiate the output structure as a copy of the first input one (reproduce fields)
[DataOut,tild,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1);
if ~isempty(errormsg)
    displ_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg],checkrun)
    return
end
time_1=[];
if isfield(DataOut,'Time')
    time_1=DataOut.Time(1);
end
if CheckNc{iview}
    if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute))
        DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute];
    end
    DataOut.Conventions='uvmat';
    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}];
    ActionKey='Action';
    while isfield(DataOut,ActionKey)
        ActionKey=[ActionKey '_1'];
    end
    DataOut.(ActionKey)=Param.Action;
    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}];
    if isfield(DataOut,'Time')
        DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}];
    end
end

%% LOOP ON SLICES
nbmissing=0; %number of undetected files
for i_slice=1:NbSlice
    index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
    nbfile=0;
    nbmissing=0;
    
    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
    for index=index_slice       
        if checkrun
            update_waitbar(hseries.Waitbar,index/(nbfield))
            stopstate=get(hseries.RUN,'BusyAction');
        else
            stopstate='queue';
        end
        
        %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
        if isequal(stopstate,'queue')% enable STOP command
            Data=cell(1,nbview);%initiate the set Data
            nbtime=0;
            dt=[];
            % loop on views (in case of multiple input series)
            for iview=1:nbview
                % reading input file(s)
                [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index));
                if ~isempty(errormsg)
                    errormsg=['time_series/read_field/' errormsg];
                    display(errormsg)
                    break
                end
                timeread(iview)=0;
                if isfield(Data{iview},'Time')
                    timeread(iview)=Data{iview}.Time;
                    nbtime=nbtime+1;
                end
                if ~isempty(NbSlice_calib)
                    Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
                end
            end
            
            % coordinate transform (or other user defined transform)
            if ~isempty(transform_fct)
                if nbview==2
                    [Data{1},Data{2}]=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
                    if isempty(Data{2})
                        Data(2)=[];
                    end
                else
                    Data{1}=transform_fct(Data{1},XmlData{1});
                end
            end
            
            % field substration (for two input file series)
            if length(Data)==2
                [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields
            else
                Field=Data{1};
            end
            if Param.CheckObject
                [Field,errormsg]=proj_field(Field,Param.ProjObject);
            end
            nbfile=nbfile+1;
            
            % initiate the time series at the first iteration
            if nbfile==1
                % stop program if the first field reading is in error
                if ~isempty(errormsg)
                    displ_uvmat('ERROR',['error in time_series/sub_field:' errormsg],checkrun)
                    return
                end
                DataOut=Field;%default
                DataOut.NbDim=Field.NbDim+1; %add the time dimension for plots
                nbvar=length(Field.ListVarName);
                if nbvar==0
                    displ_uvmat('ERROR','no input variable selected in get_field',checkrun)
                    return
                end
                testsum=2*ones(1,nbvar);%initiate flag for action on each variable
                if isfield(Field,'VarAttribute') % look for coordinate and flag variables
                    for ivar=1:nbvar
                        if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role')
                            var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable
                            if isequal(var_role,'errorflag')
                                displ_uvmat('ERROR','do not handle error flags in time series',checkrun)
                                return
                            end
                            if isequal(var_role,'warnflag')
                                testsum(ivar)=0;  % not recorded variable
                                eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable
                            end
                            if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|...
                                    isequal(var_role,'coord_z')|isequal(var_role,'coord')
                                testsum(ivar)=1; %constant coordinates, record without time evolution
                            end
                        end
                        % check whether the variable ivar is a dimension variable
                        DimCell=Field.VarDimName{ivar};
                        if ischar(DimCell)
                            DimCell={DimCell};
                        end
                        if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables
                            testsum(ivar)=1;
                        end
                    end
                end
                for ivar=1:nbvar
                    if testsum(ivar)==2
                        eval(['DataOut.' Field.ListVarName{ivar} '=[];'])
                    end
                end
                DataOut.ListVarName=[{'Time'} DataOut.ListVarName];
            end
            
            % add data to the current field
            for ivar=1:length(Field.ListVarName)
                VarName=Field.ListVarName{ivar};
                VarVal=Field.(VarName);
                if testsum(ivar)==2% test for recorded variable
                    if isempty(errormsg)
                        if isequal(Param.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode
                            if isempty(VarVal)
                                displ_uvmat('ERROR',['empty result at frame index ' num2str(i1_series{iview}(index))],checkrun)
                                return
                            end
                            VarVal=mean(VarVal,1);
                        end
                        VarVal=shiftdim(VarVal,-1); %shift dimension
                        DataOut.(VarName)=cat(1,DataOut.(VarName),VarVal);%concanete the current field to the time series
                    else
                        DataOut.(VarName)=cat(1,DataOut.(VarName),0);% put each variable to 0 in case of input reading error
                    end
                elseif testsum(ivar)==1% variable representing fixed coordinates
                    eval(['VarInit=DataOut.' VarName ';']);
                    if isempty(errormsg) && ~isequal(VarVal,VarInit)
                        displ_uvmat('ERROR',['time series requires constant coordinates ' VarName],checkrun)
                        return
                    end
                end
            end
            
            % record the time:
            if isempty(time)% time read in ncfiles
                if isfield(Field,'Time')
                    DataOut.Time(nbfile,1)=Field.Time;
                else
                    DataOut.Time(nbfile,1)=index;%default
                end
            else % time from ImaDoc prevails  TODO: correct
                DataOut.Time(nbtime,1)=i1_series{1}(index);% TODO : generalise
            end
            
            % record the number of missing input fields
            if ~isempty(errormsg)
                nbmissing=nbmissing+1;
                display(['index=' num2str(index) ':' errormsg])
            end
        end
    end
    %%%%%%% END OF LOOP WITHIN A SLICE
    
    %remove time for global attributes if exists
    Time_index=find(strcmp('Time',DataOut.ListGlobalAttribute));
    if ~isempty(Time_index)
        DataOut.ListGlobalAttribute(Time_index)=[];
    end
    DataOut.Conventions='uvmat';
    for ivar=1:numel(DataOut.ListVarName)
        VarName=DataOut.ListVarName{ivar};
        eval(['DataOut.' VarName '=squeeze(DataOut.' VarName ');']) %remove singletons
    end
    
    % add time dimension
    for ivar=1:length(Field.ListVarName)
        DimCell=Field.VarDimName(ivar);
        if testsum(ivar)==2%variable used as time series
            DataOut.VarDimName{ivar}=[{'Time'} DimCell];
        elseif testsum(ivar)==1
            DataOut.VarDimName{ivar}=DimCell;
        end
    end
    indexremove=find(~testsum);
    if ~isempty(indexremove)
        DataOut.ListVarName(1+indexremove)=[];
        DataOut.VarDimName(indexremove)=[];
        if isfield(DataOut,'Role') && ~isempty(DataOut.Role{1})%generaliser aus autres attributs
            DataOut.Role(1+indexremove)=[];
        end
    end
    
    %shift variable attributes
    if isfield(DataOut,'VarAttribute')
        DataOut.VarAttribute=[{[]} DataOut.VarAttribute];
    end
    DataOut.VarDimName=[{'Time'} DataOut.VarDimName];
    DataOut.Action=Param.Action;%name of the processing programme
    test_time=diff(DataOut.Time)>0;% test that the readed time is increasing (not constant)
    if ~test_time
        DataOut.Time=[1:filecounter];
    end
    
    % display nbmissing
    if ~isequal(nbmissing,0)
        displ_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'],checkrun)
    end
    
    %name of result file
    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),i_slice,[]);
    errormsg=struct2nc(OutputFile,DataOut); %save result file
    if isempty(errormsg)
        display([OutputFile ' written'])
    else
        displ_uvmat('ERROR',['error in Series/struct2nc: ' errormsg],checkrun)
    end
end

%% plot the time series (the last one in case of multislices)
if checkrun
    figure
    haxes=axes;
    plot_field(DataOut,haxes)
       
    %% display the result file using the GUI get_field
    hget_field=findobj(allchild(0),'name','get_field');
    if ~isempty(hget_field)
        delete(hget_field)
    end
    get_field(OutputFile,DataOut)
end