%'sub_background': substract a sliding background to an image series
%------------------------------------------------------------------------
% Method: 
    %calculate the background image by sorting the luminosity of each point
    % over a sliding sub-sequence of 'nbaver_ima' images. 
    % The luminosity value of rank 'rank' is selected as the
    % 'background'. rank=nbimages/2 gives the median value.  Smaller values are appropriate
    % for a dense set of particles. The extrem value rank=1 gives the true minimum
    % luminosity, but it can be polluted by noise. 
% Organization of image indices:
    % The program is working on a series of images, 
    % In the mode 'volume', nbfield2=1 (1 image at each level)and NbSlice (=NbField_j)
    % Else nbfield2=NbField_j =nbre of images in a burst (j index)
    
% function GUI_config=sub_background(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 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
%   http://www.legi.grenoble-inp.fr
%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.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=sub_background (Param)

%%%%%%%%%%%%%%%%%    INPUT PREPARATION MODE (no RUN)    %%%%%%%%%%%%%%%%%
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='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
    ParamOut.NbSlice='on'; % edit box nbre of slices made active
    ParamOut.VelType='off';% 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 (option 'off'/'on','off' by default)
    ParamOut.ProjObject='off';%cannot use projection object(option 'off'/'on','off' by default)
    ParamOut.Mask='off';%cannot use mask option   (option 'off'/'on', 'off' by default)
    ParamOut.OutputDirExt='.sback';%set the output dir extension
    ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice

    %% check the validity of  input file types
    if isfield(Param,'SeriesData')&& isfield(Param.SeriesData,'FileInfo')
    if ~strcmp(Param.SeriesData.FileInfo{1}.FieldType,'image')
        msgbox_uvmat('ERROR','invalid file type input: not an image series')
        return
    end
    end

    %% numbers of fields
    NbSlice_i=1;%default
    if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
        NbSlice_i=Param.IndexRange.NbSlice;
    end
    incr_j=1;%default
    if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j)
        incr_j=Param.IndexRange.incr_j;
    end
    if isfield(Param.IndexRange,'first_j')&&~isempty(Param.IndexRange.first_j)
        NbField_j=numel(Param.IndexRange.first_j:incr_j:Param.IndexRange.last_j);%nb of fields for the j index (bursts or volume slices)
    else
        NbField_j=1;
    end
    first_i=1;last_i=1;incr_i=1;%default
    if isfield(Param.IndexRange,'MinIndex_i'); first_i=Param.IndexRange.MinIndex_i; end   
    if isfield(Param.IndexRange,'MaxIndex_i'); last_i=Param.IndexRange.MaxIndex_i; end
    if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i)
        incr_i=Param.IndexRange.incr_i;
    end
    nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices)
    nbfield=NbField_j*nbfield_i; %total number of fields
    nbfield_i=floor(nbfield/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
    
    %% setting of  parameters specific to sub_background
    CheckVolume='No';
    nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts 
    SaturationValue=0;
     if nbfield_i~=1 && NbField_j<=nbaver_init
        nbaver=floor(nbaver_init/NbField_j); % number of bursts used for the sliding background,
        if isequal(mod(nbaver,2),0)% if nbaver is even
            nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined)
        end
        nbaver_init=nbaver*NbField_j;%propose by default an integer number of bursts
    end
    BrightnessRankThreshold=0.1;
    if isfield(Param,'ActionInput')
        if isfield(Param.ActionInput,'CheckVolume') && Param.ActionInput.CheckVolume
            CheckVolume='Yes';
        end
        if isfield(Param.ActionInput,'SlidingSequenceLength')
         nbaver_init=Param.ActionInput.SlidingSequenceLength;
        end
        if isfield(Param.ActionInput,'BrightnessRankThreshold')
          BrightnessRankThreshold=Param.ActionInput.BrightnessRankThreshold;
        end
        if isfield(Param.ActionInput,'SaturationValue') 
            SaturationValue=Param.ActionInput.SaturationValue;
        end
    end   
    prompt = {'volume scan mode (Yes/No)';...
        'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';...
        'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles';...
        'image saturation level for rescaling( reduce the influence of particles brighter than this value), =0 for no rescaling' };
    dlg_title = 'get (slice by slice) a sliding background and substract to each image';
    num_lines= 4;
    def     = { CheckVolume;num2str(nbaver_init);num2str(BrightnessRankThreshold);num2str(SaturationValue)};
    answer = inputdlg(prompt,dlg_title,num_lines,def);
    if isempty(answer)
        return
    end
    %check input consistency
    if strcmp(answer{1},'No') && ~isequal(NbSlice_i,1)
        check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice_i) ' slices']);
        if ~strcmp(check,'Yes')
            return
        end
    end
    if strcmp(answer{1},'Yes')
        step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume 
        ParamOut.NbSlice=1; %nbre of slices displayed 
    else
        step=NbField_j;%case of bursts: the sliding background is shifted by the length of one burst
    end
    ParamOut.ActionInput.SlidingSequenceLength=adjust_slidinglength(str2double(answer{2}),step);
    ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes');
    ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3});
%     ParamOut.ActionInput.CheckSubmedian=strcmp(answer{4},'Yes');
    ParamOut.ActionInput.SaturationValue=str2double(answer{4});
    % apply the image rescaling function 'level' (avoid the blinking effects of bright particles)
%     answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background');
%     ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes');
    return
end
%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%% 

%% read input parameters from an xml file if input is a file name (batch mode)
% checkrun=1;
RUNHandle=[];
% WaitbarHandle=[];
if ischar(Param)
    Param=xml2struct(Param);% read Param as input file (batch case)
else
 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
end

%% input preparation
NbSlice_i=Param.IndexRange.NbSlice;
if ~isequal(NbSlice_i,1)
    disp(['multi-level splitting into ' num2str(NbSlice_i) ' slices']);
end
RootPath=Param.InputTable{1,1};
RootFile=Param.InputTable{1,3};
SubDir=Param.InputTable{1,2};
NomType=Param.InputTable{1,4};
FileExt=Param.InputTable{1,5};
%[filecell,i1_series,i2_series,j1_series]=get_file_series(Param);%series of file names organised as a single array


%% file index parameters
% NbSlice_i: nbre of slices for i index in multi-level mode: equal to 1 for a single level
% the function sub_background is then relaunched by the GUI series for each
%      slice, incrementing the first index i by 1
% NbSlice_j: nbre of slices in volume mode
% nbfield : total number of images treated per slice
% step: shift of image index at each step of the sliding background (corresponding to the nbre of images in a burst)
% nbaver_ima: nbre of the images in the sliding sequence used for the background
% nbaver=nbaver_ima/step: nbre of bursts corresponding to nbaver_ima images. It has been adjusted so that nbaver is an odd integer
i_indices=Param.IndexRange.first_i:Param.IndexRange.incr_i:Param.IndexRange.last_i;
if isfield(Param.IndexRange,'first_j')
j_indices=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j;
else
    j_indices=1;
end
nbfield_i=numel(i_indices); %nb of fields for the i index (bursts or volume slices)
NbField_j=numel(j_indices); %nb of fields for the j index
j_indices=j_indices'*ones(1,nbfield_i);
i_indices=ones(NbField_j,1)*i_indices;

if Param.ActionInput.CheckVolume% case of volume scan: the background images must be determined for each index j
    step=2;% we assume the burst contains only one image pair
    NbSlice_j=NbField_j;
    nbfield_series=nbfield_i;
else 
    if Param.ActionInput.SlidingSequenceLength<NbField_j
        step=1;
    else
    step=NbField_j;%case of bursts: the sliding background is shifted by the length of one burst
    end
    NbSlice_j=1;
    nbfield_series=nbfield_i*NbField_j;
end
nbfield=NbField_j*nbfield_i; %total number of fields
[nbaver_ima,nbaver,step]=adjust_slidinglength(Param.ActionInput.SlidingSequenceLength,step);
if nbaver_ima > nbfield
    disp('number of images in a slice smaller than the proposed number of images for the sliding average')
    return
end
halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background 


%% File relabeling documented by the xml file
CheckRelabel=isfield(Param.IndexRange,'Relabel' )&& Param.IndexRange.Relabel;%=true for index relabeling (PCO);

%% Input file info
if CheckRelabel
    XmlFileName=find_imadoc(RootPath,SubDir);
    if ~isempty(XmlFileName)
        XmlData=imadoc2struct(XmlFileName);%read the time from XmlFileName
    end
   % RootFileOut=index2filename(XmlData.FileSeries,1,1,MaxIndex_j);
    [RootFileOut,frame_index]=index2filename(XmlData.FileSeries,Param.IndexRange.first_i,j_indices(1),NbField_j);
    FirstFileName=fullfile(RootPath,SubDir,RootFileOut);
else
    FirstFileName=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,Param.IndexRange.first_i,[],j_indices(1));%get first file name
    RootFileOut=RootFile;
end
[FileInfo,MovieObject]=get_file_info(FirstFileName);
FileType=FileInfo.FileType;
if ~CheckRelabel
    if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1
        if isempty(regexp(NomType,'1$', 'once'))% no file indexing
            frame_index=i_indices;% the index i denotes the frame number in a movie, no index j
        else
            frame_index=j_indices;% the index j denotes the frame number in a movie
            MovieObject=[]; %not a single video object
        end
    else
        frame_index=ones(1,nbfield);
    end
end

%% output file naming
FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image'
if strcmp(FileInfo.FileType,'image')
    NomTypeOut=NomType;
elseif NbField_j==1
    NomTypeOut='_1';
else
    NomTypeOut='_1_1';% case of purely numerical indexing
end
OutputDir=[Param.OutputSubDir Param.OutputDirExt];
OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);

%% calculate absolute brightness rank
rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima);
if rank==0
    rank=1;%rank selected in the sorted image series
end

%% prealocate memory for the sliding background
Ak=zeros(FileInfo.Height,FileInfo.Width,nbaver_ima,['uint' num2str(FileInfo.BitDepth)]); %prealocate memory

%% selection of frame indices
if Param.ActionInput.CheckVolume
    nbfield=floor(nbfield/NbSlice_j)*NbSlice_j;% truncate the total number of frames in case of incomplete series
    indselect=1:nbfield;
    indselect=reshape(indselect,NbSlice_j,[]);
    NbSlice=NbSlice_j;
else
    NbSlice=NbSlice_i;
    nbfield=floor(nbfield/NbSlice)*NbSlice;% truncate the total number of frames in case of incomplete series
    indselect=reshape(1:nbfield,NbSlice,[]);
    for j_slice=1:NbSlice
        indselect(j_slice,:)=j_slice:NbSlice:nbfield;% select file indices of the slice
    end
end

%%%%%%%  LOOP ON SLICES %%%%%%%
for j_slice=1:NbSlice

    %% read the first series of nbaver_ima images and sort by luminosity at each pixel
    for ifield = 1:nbaver_ima
        ifile=indselect(j_slice,ifield);
        %filename=filecell{1,ifile};
        if CheckRelabel
            [filename,FrameIndex]=index2filename(XmlData.FileSeries,i_indices(ifile),j_indices(ifile),NbField_j);
             filename=fullfile(RootPath,SubDir,filename);
        else
            filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i_indices(ifile),[],j_indices(ifile));
            FrameIndex=frame_index(ifile);
        end
        Aread=read_image(filename,FileType,MovieObject,FrameIndex);
        if ndims(Aread)==3%color images
            Aread=sum(double(Aread),3);% take the sum of color components
        end
        Ak(:,:,ifield)=Aread;
    end
    Asort=sort(Ak,3);%sort the luminosity of images at each point
    B=Asort(:,:,rank);%background image

    %% substract the first background image to the first images
    disp( 'first background image will be substracted')
    for ifield=1:step*(halfnbaver+1)% nbre of images treated by the first background image
        Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
        ifile=indselect(j_slice,ifield);
        newname=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_indices(ifile),[],j_indices(ifile));

        %write result file
        if ~isequal(Param.ActionInput.SaturationValue,0)
            he=levels(Acor,Param.ActionInput.SaturationValue);
            imwrite(C,newname,'BitDepth',16); % save the new image
        else
            if isequal(FileInfo.BitDepth,16)
                C=uint16(Acor);
                imwrite(C,newname,'BitDepth',16); % save the new image
            else
                C=uint8(Acor);
                imwrite(C,newname,'BitDepth',8); % save the new image
            end
        end
        disp([newname ' written'])
    end

    %% repeat the operation on a sliding series of images
    disp('sliding background image will be substracted')
    if nbfield_series > nbaver_ima
        for ifield = step*(halfnbaver+1):step:nbfield_series-step*(halfnbaver+1)% ifield +iburst=index of the current processed image
            %             update_waitbar(WaitbarHandle,ifield/nbfield_series)
            if  ~isempty(RUNHandle)&&~strcmp(get(RUNHandle,'BusyAction'),'queue')
                disp('program stopped by user')
                return
            end
            if nbaver_ima>step
                Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
            end
            %incorporate next burst in the current image series
            for iburst=1:step
                ifile=indselect(j_slice,ifield+iburst+step*halfnbaver);
                if CheckRelabel
                    [filename,FrameIndex]=index2filename(XmlData.FileSeries,i_indices(ifile),j_indices(ifile),NbField_j);
                    filename=fullfile(RootPath,SubDir,filename);
                else
                    filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i_indices(ifile),[],j_indices(ifile));
                    FrameIndex=frame_index(ifile);
                end
                Aread=read_image(filename,FileType,MovieObject,FrameIndex);
                if ndims(Aread)==3%case of color images
                    Aread=sum(double(Aread),3);% take the sum of color components
                end
                Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image
            end
            Asort=sort(Ak,3);%sort the new current image series by luminosity
            B=Asort(:,:,rank);%current background image
            %substract the background for the current burst
            for iburst=1:step
                Acor=double(Ak(:,:,step*halfnbaver+iburst))-double(B); %the current image has been already read ans stored as index step*halfnbaver+iburst in the current series
                Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
                ifile=indselect(j_slice,ifield+iburst);
                newname=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_indices(ifile),[],j_indices(ifile));
                %write result file
                if ~isequal(Param.ActionInput.SaturationValue,0)
                    C=levels(Acor,Param.ActionInput.SaturationValue);
                    imwrite(C,newname,'BitDepth',16); % save the new image
                else
                    if isequal(FileInfo.BitDepth,16)
                        C=uint16(Acor);
                        imwrite(C,newname,'BitDepth',16); % save the new image
                    else
                        C=uint8(Acor);
                        imwrite(C,newname,'BitDepth',8); % save the new image
                    end
                end
                disp([newname ' written'])
            end
        end
    end

    %% substract the background from the last images
    disp('last background image will be substracted')
    for  ifield=nbfield_series-step*halfnbaver+1:nbfield_series
        Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B);
        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
        ifile=indselect(j_slice,ifield);
        newname=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_indices(ifile),[],j_indices(ifile));
        %write result file
        if ~isequal(Param.ActionInput.SaturationValue,0)
            C=levels(Acor,Param.ActionInput.SaturationValue);
            imwrite(C,newname,'BitDepth',16); % save the new image
        else
            if isequal(FileInfo.BitDepth,16)
                C=uint16(Acor);
                imwrite(C,newname,'BitDepth',16); % save the new image
            else
                C=uint8(Acor);
                imwrite(C,newname,'BitDepth',8); % save the new image
            end
        end
        disp([newname ' written'])
    end
end

function C=levels(A,Coeff)

% nblock_y=100;%2*Param.TransformInput.BlockSize;
% nblock_x=100;%2*Param.TransformInput.BlockSize;
% [npy,npx]=size(A);
% [X,Y]=meshgrid(1:npx,1:npy);
% 
% %Backg=zeros(size(A));
% %Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
% %Amin=A.*Aflagmin;%values of A at local minima
% % local background: find all the local minima in image subblocks
% if CheckSubmedian
%     fctblock= inline('median(x(:))');
%     Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in  blocks
%     %B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
%     A=A-imresize(Backg,size(A),'bilinear');% substract background interpolated to the initial size image
% end
% fctblock= inline('mean(x(:))');
% AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
% fctblock= inline('var(x(:))');
% AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
% Avalue=AVar./AMean;% typical value of particle luminosity
% Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image
%C=uint16(1000*tanh(A./(Coeff*Avalue)));
C=uint16(Coeff*tanh(A./Coeff));
%------------------------------------------
% adjust the number of images used for the sliding average
function [nbaver_ima,nbaver,step_out]=adjust_slidinglength(nb_aver_in,step)
%nbaver_ima=str2double(nb_aver_in);%number of images for the sliding background
nbaver=ceil(nb_aver_in/step);%number of bursts for the sliding background
if isequal(mod(nbaver,2),0)% if nbaver is even
    nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
end
step_out=step;
if nbaver>1
    nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver
else
    nbaver_ima=nb_aver_in;
    if isequal(mod(nbaver_ima,2),0)% if nbaver_ima is even
        nbaver_ima=nbaver_ima+1;%set the number of bursts to an odd number (so the middle burst is defined)
    end
    step_out=1;
end
