%'aver_stat': calculate Reynolds steress components over time series
%------------------------------------------------------------------------
% function ParamOut=turb_stat(Param)
%
%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%OUTPUT
% ParamOut: sets 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
% when Param.Action.RUN=0 (as activated when the current Action is selected
% in series), the function ouput paramOut 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
%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
%             .RUN =0 for GUI input, =1 for function activation
%             .RunMode='local','background', 'cluster': type of function  use
%             
%    .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
%    .InputFields: sub structure describing the input fields withfields
%              .FieldName: name(s) 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
%              .Coord_y: name of y coordinate variable
%              .Coord_x: name of x coordinate variable
%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%=======================================================================
% Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
%   http://www.legi.grenoble-inp.fr
%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
%
%     This file is part of the toolbox UVMAT.
%
%     UVMAT is free software; you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published
%     by the Free Software Foundation; either version 2 of the license,
%     or (at your option) any later version.
%
%     UVMAT is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License (see LICENSE.txt) for more details.
%=======================================================================

function ParamOut=turb_stat(Param)

%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
if isstruct(Param) && isequal(Param.Action.RUN,0)
    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
    ParamOut.NbSlice='on'; %nbre of slices ('on' if needed as input, fixed value e.g. 1, 'off' by default)
    ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
    ParamOut.FieldTransform = 'off';%can use a transform function
    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
    ParamOut.OutputDirExt='.staturb';%set the output dir extension
    ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
%     filecell=get_file_series(Param);%check existence of the first input file
%     if ~exist(filecell{1,1},'file')
%         msgbox_uvmat('WARNING','the first input file does not exist')
%     end
    return
end

%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
ParamOut=[];%default output
%% read input parameters from an xml file if input is a file name (batch mode)
checkrun=1;
if ischar(Param)
    Param=xml2struct(Param);% read Param as input file (batch case)
    checkrun=0;
end
hseries=findobj(allchild(0),'Tag','series');
RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series

%% define the directory for result file (with path=RootPath{1})
OutputDir=[Param.OutputSubDir Param.OutputDirExt];
    
%% root input file(s) name, type and index series
RootPath=Param.InputTable(:,1);
RootFile=Param.InputTable(:,3);
SubDir=Param.InputTable(:,2);
NomType=Param.InputTable(:,4);
FileExt=Param.InputTable(:,5);
[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
%%%%%%%%%%%%
% The cell array filecell is the list of input file names, while
% filecell{iview,fileindex}:
%        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
%%%%%%%%%%%% NbView=1 : a single input series
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

%% determine the file type on each line from the first input file 
NcTypeOptions={'netcdf','civx','civdata'};
for iview=1:NbView
    if ~exist(filecell{iview,1}','file')
        msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'])
        return
    end
    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
    FileType{iview}=FileInfo{iview}.FileType;
    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=[];
[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
        msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
    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

%% settings for the output file
FileExtOut='.nc';% write result as .nc files for netcdf inputs
NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
first_i=i1_series{1}(1);
last_i=i1_series{1}(end);
if isempty(j1_series{1})% if there is no second index j
    first_j=1;last_j=1;
else
    first_j=j1_series{1}(1);
    last_j=j1_series{1}(end);
end

%% Set field names and velocity types
InputFields{1}=[];%default (case of images)
if isfield(Param,'InputFields')
    InputFields{1}=Param.InputFields;
end
if isempty(InputFields{1}.FieldName)
    disp('ERROR: input fields U, V and posibly curl and div must be entered by get_field...')
    return
end

nbfiles=0;
nbmissing=0;

%initialisation
DataOut.ListGlobalAttribute= {'Conventions'};
DataOut.Conventions= 'uvmat';
DataOut.ListVarName={};
DataOut.VarDimName={};
DataOut.UMean=0;
DataOut.VMean=0;
DataOut.u2Mean=0;
DataOut.v2Mean=0;
DataOut.u2Mean_1=0;
DataOut.v2Mean_1=0;
DataOut.uvMean=0;
DataOut.Counter=0;
DataOut.CurlMean=0;
DataOut.DivMean=0;
DataOut.Curl2Mean=0;
DataOut.Div2Mean=0;
DataOut.KEflux=0;
U2Mean=0;
V2Mean=0;
UVMean=0;
U2Mean_1=0;
V2Mean_1=0;
Counter_1=0;

%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
% for i_slice=1:Param.IndexRange.NbSlice
%     i_slice
    ind_first=Param.IndexRange.first_i;
    for index_i=ind_first:Param.IndexRange.NbSlice:Param.IndexRange.last_i
        if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
            disp('program stopped by user')
            break
        end
        for index_j=first_j:last_j
            InputFile=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},index_i,index_i,index_j,index_j);
            [Field,tild,errormsg] = read_field(InputFile,FileType{iview},InputFields{iview});
            
            %[Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
            
            %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
            if index_i==ind_first && index_j==first_j %initiate the output data structure in the first field
                [CellInfo,NbDim,errormsg]=find_field_cells(Field);
                YName='coord_y';%default
                XName='coord_x';%default
                for icell=1:numel(NbDim)
                    if NbDim(icell)==2 && strcmp(CellInfo{icell}.CoordType,'grid')
                        YName=CellInfo{icell}.YName;
                        XName=CellInfo{icell}.XName;
                        break
                    end
                end
                DataOut.ListVarName={YName, XName ,'UMean' , 'VMean','u2Mean','v2Mean','u2Mean_1','v2Mean_1','uvMean','CurlMean','DivMean','Curl2Mean','Div2Mean','Counter'};
                DataOut.VarDimName={YName,XName,{YName,XName},{YName,XName},{YName,XName},{YName,XName},{YName,XName},{YName,XName},...
                    {YName,XName},{YName,XName},{YName,XName},{YName,XName},{YName,XName},{YName,XName}};
                DataOut.(YName)=Field.(YName);
                DataOut.(XName)=Field.(XName);
                Uprev=Field.U;% store the current field for next iteration
                Vprev=Field.V;
                if isfield(Field,'FF')
                    FFprev=Field.FF;% possible flag for false data
                else
                    %FFprev=true(size(Field.U));
                    FFprev=isnan(Field.U);
                end
            end
            FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U
            DataOut.Counter=DataOut.Counter+ (~FF);% add 1 to the couter for non NaN point
            Counter_1=Counter_1+(~FF & ~FFprev);
            Field.U(FF)=0;% set to 0 the nan values
            Field.V(FF)=0;
            DataOut.UMean=DataOut.UMean+Field.U; %increment the sum
            DataOut.VMean=DataOut.VMean+Field.V; %increment the sum
            
            U2Mean=U2Mean+(Field.U).*(Field.U); %increment the U squared sum
            V2Mean=V2Mean+(Field.V).*(Field.V); %increment the V squared sum
            UVMean=UVMean+(Field.U).*(Field.V); %increment the sum
            U2Mean_1=U2Mean_1+(Field.U).*Uprev; %increment the U squared sum
            V2Mean_1=V2Mean_1+(Field.V).*Vprev; %increment the V squared sum
            Uprev=Field.U; %store for next iteration
            Vprev=Field.V;
            FFprev=FF;
            if isfield(Field,'curl') && isfield(Field,'div')
                Field.curl(FF)=0;% set to 0 the nan values
                Field.div(FF)=0;
                DataOut.CurlMean=DataOut.CurlMean+Field.curl;
                DataOut.DivMean=DataOut.DivMean+Field.div;
                DataOut.Curl2Mean=DataOut.Curl2Mean+Field.curl.*Field.curl;
                DataOut.Div2Mean=DataOut.Div2Mean+Field.div.*Field.div;
            end
        end
    end
    %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
    
    DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero
    DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean
    DataOut.VMean=DataOut.VMean./DataOut.Counter; % normalize the mean
    U2Mean=U2Mean./DataOut.Counter; % normalize the mean
    V2Mean=V2Mean./DataOut.Counter; % normalize the mean
    UVMean=UVMean./DataOut.Counter; % normalize the mean
    U2Mean_1=U2Mean_1./Counter_1; % normalize the mean
    V2Mean_1=V2Mean_1./Counter_1; % normalize the mean
    DataOut.u2Mean=U2Mean-DataOut.UMean.*DataOut.UMean; % normalize the mean
    DataOut.v2Mean=V2Mean-DataOut.VMean.*DataOut.VMean; % normalize the mean
    DataOut.uvMean=UVMean-DataOut.UMean.*DataOut.VMean; % normalize the mean \
    DataOut.u2Mean_1=U2Mean_1-DataOut.UMean.*DataOut.UMean; % normalize the mean
    DataOut.v2Mean_1=V2Mean_1-DataOut.VMean.*DataOut.VMean; % normalize the mean
    DataOut.CurlMean=DataOut.CurlMean./DataOut.Counter;
    DataOut.DivMean=DataOut.DivMean./DataOut.Counter;
    DataOut.Curl2Mean=DataOut.Curl2Mean./DataOut.Counter-DataOut.CurlMean.*DataOut.CurlMean;
    DataOut.Div2Mean=DataOut.Div2Mean./DataOut.Counter-DataOut.DivMean.*DataOut.DivMean;    
    
    %% writing the result file as netcdf file
    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,ind_first,ind_first,first_j,last_j);
    %case of netcdf input file , determine global attributes
    errormsg=struct2nc(OutputFile,DataOut); %save result file
    if isempty(errormsg)
        disp([OutputFile ' written']);
    else
        disp(['error in writting result file: ' errormsg])
    end
    
% end
%% open the result file with uvmat (in RUN mode)
if checkrun && isequal(Param.IndexRange.NbSlice,1)
    uvmat(OutputFile)% open the last result file with uvmat
end