%'aver_stat': calculate field average over a time series
%------------------------------------------------------------------------
% function ParamOut=aver_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)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function ParamOut=aver_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 ('off' by default)
    ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
    ParamOut.FieldName='two';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
    ParamOut.FieldTransform = 'on';%can use a transform function
    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
    ParamOut.OutputDirExt='.stat';%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=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 
ImageTypeOptions={'image','multimage','mmreader','video'};
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
    [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
        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

%% 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
    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
    return
end
if nbview==2 && ~isequal(CheckImage{1},CheckImage{2})
    msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
    return
end

%% settings for the output file
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 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

% for i_slice=1:NbSlice
% index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
nbfiles=0;
nbmissing=0;

%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
for index=1:nbfield
    update_waitbar(WaitbarHandle,index/nbfield)
    if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
        disp('program stopped by user')
        break
    end
    
    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
    for iview=1:nbview
        % reading input file(s)
        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
        if ~isempty(errormsg)
            errormsg=['error of input reading: ' errormsg];
            break
        end
        if ~isempty(NbSlice_calib)
            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
        end
    end
    %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
    %%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
    % EDIT FROM HERE
    
    if isempty(errormsg)
        Field=Data{1}; % default input field structure
        %% coordinate transform (or other user defined transform)
        if ~isempty(transform_fct)
            switch nargin(transform_fct)
                case 4
                    if length(Data)==2
                        Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
                    else
                        Field=transform_fct(Data{1},XmlData{1});
                    end
                case 3
                    if length(Data)==2
                        Field=transform_fct(Data{1},XmlData{1},Data{2});
                    else
                        Field=transform_fct(Data{1},XmlData{1});
                    end
                case 2
                    Field=transform_fct(Data{1},XmlData{1});
                case 1
                    Field=transform_fct(Data{1});
            end
        end
        
        %% calculate tps coefficients if needed
        if isfield(Param,'ProjObject')&&isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps')
            Field=tps_coeff_field(Field,check_proj_tps);
        end
        
        %field projection on an object
        if Param.CheckObject
            [Field,errormsg]=proj_field(Field,Param.ProjObject);
            if ~isempty(errormsg)
                msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg])
                return
            end
        end
        nbfiles=nbfiles+1;
        
        %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
        if nbfiles==1 %first field
            time_1=[];
            if isfield(Field,'Time')
                time_1=Field.Time(1);
            end
            DataOut=Field;%default
            for ivar=1:length(Field.ListVarName)
                VarName=Field.ListVarName{ivar};
                DataOut.(VarName)=double(DataOut.(VarName));
            end
        else   %current field
            for ivar=1:length(Field.ListVarName)
                VarName=Field.ListVarName{ivar};
                sizmean=size(DataOut.(VarName));
                siz=size(Field.(VarName));
                if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
                    displ_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
                    return
                else
                    DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
                end
            end
        end
        %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
    else
        disp(errormsg)
    end
end
%%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%

for ivar=1:length(Field.ListVarName)
    VarName=Field.ListVarName{ivar};
    DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean
end
if nbmissing~=0
    msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'])
end
if isempty(time) % time is read from files
    if isfield(Field,'Time')
        time_end=Field.Time(1);%last time read
        if ~isempty(time_1)
            DataOut.Time=time_1;
            DataOut.Time_end=time_end;
        end
    end
else  % time from ImaDoc prevails if it exists
    DataOut.Time=time(1);
    DataOut.Time_end=time(end);
end

%% writing the result file
OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j);
if CheckImage{1} %case of images
    if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
        DataOut.A=uint16(DataOut.A);
        imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
    else
        DataOut.A=uint8(DataOut.A);
        imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
    end
    disp([OutputFile ' written']);
else %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  % end averaging  loop

%% open the result file with uvmat (in RUN mode)
if checkrun
%     hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
%     delete(hget_field)
    uvmat(OutputFile)% open the last result file with uvmat
end