%'sub_background': substract background to an image series, used with series.fig
%------------------------------------------------------------------------
% function GUI_input=sub_background(Param)
%
%OUTPUT
% GUI_input=list of options in the GUI series.fig needed for the function
%
%INPUT:
%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
%Series: Matlab structure containing information set by the series interface
%       .RootPath: path to the image series
%       .RootFile: root file name
%       .FileExt: image file extension 
%       .NomType: nomenclature type for file indexing
%       .NbSlice: %number of slices defined on the interface
%----------------------------------------------------------------------
% 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, labelled by two indices i and j, given 
    % by the input matlab vectors num_i1 and num_j1 respectively. In the list, j is the fastest increasing index.
    % The processing can be done in slices (number nbslice), with bursts of
    % nbfield2 successive images for a given slice (mode 'multilevel')
    % In the mode 'volume', nbfield2=1 (1 image at each level)
%
function GUI_input=sub_background (Param)

%------------------------------------------------------------------------
%requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
if ~exist('Param','var')
    GUI_input={'RootPath';'on';...
        'SubDir';'off';... % subdirectory of derived files (PIV fields), ('on' by default)
        'RootFile';'on';... %root input file name ('on' by default)
        'FileExt';'on';... %inputf file extension ('on' by default)
        'NomType';'on';...%type of file indexing ('on' by default)
        'NbSlice';'on'; ...%nbre of slices ('off' by default)
        %'VelTypeMenu';'on';...% menu for selecting the velocity type (civ1,..)('off' by default)
        %'FieldMenu';'on';...% menu for selecting the velocity field (s) in the input file ('off' by default)
        %'VelTypeMenu_1';'on';...% menu for selecting the velocity type (civ1,..)('off' by default)
        %'FieldMenu_1';'on';...% menu for selecting the velocity field (s) in the input file ('off' by default)
        %'CoordType';...%can use a transform function
        %'GetObject';...;%can use projection object
        %'GetMask';...;%can use mask option  
        %'PARAMETER';'NbSliding';...
        %'PARAMETER';'VolumeScan';...
        %'PARAMETER';'RankBrightness';...
               ''};
    return %exit the function 
end

%% input parameters
% read the xml file for batch case
if ischar(Param) && ~isempty(find(regexp('Param','.xml$')))
    Param=xml2struct(Param);
else %  RUN case: parameters introduced as the input structure Param
    hseries=guidata(Param.hseries);%handles of the GUI series
    WaitbarPos=get(hseries.waitbar_frame,'Position');
end
filebase=fullfile(Param.InputTable{1,1},Param.InputTable{1,3});
dir_images=Param.InputTable{1,1};
NomType=Param.InputTable{1,4};
FileExt=Param.InputTable{1,5};
[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
if size(filecell,1)>1
    msgbox_uvmat('WARNING','This function uses only the first input image series')
    return
end

%%% TODO: update with the new conventions%%%%%%%%%%%%%%%%%
%% determine input image type
FileType=[];%default
MovieObject=[];
%FileExt=Series.FileExt;

if isequal(lower(FileExt),'.avi')
    hhh=which('mmreader');
    if ~isequal(hhh,'')&& mmreader.isPlatformSupported()
        MovieObject=mmreader(fullfile(RootPath,[RootFile FileExt]));
        FileType='movie';
    else
        FileType='avi';
    end
elseif isequal(lower(FileExt),'.vol')
    FileType='vol';
else
    form=imformats(FileExt(2:end));
    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
        if isequal(NomType,'*');
            FileType='multimage';
        else
            FileType='image';
        end
    end
end
if isempty(FileType)
    msgbox_uvmat('ERROR',['invalid file extension ' FileExt ': this function only accepts image or movie input'])
    return
end

nbslice_i=Param.NbSlice; %number of slices
siz=size(i1_series{1});
nbaver_init=23;%approximate number of images used for the sliding background: to be adjusted later to include an integer number of bursts
j1=[];%default

%% 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');
test_level=isequal(answer,'Yes');

%% adjust the proposed number of images in the sliding average to include an integer number of bursts
if siz(2)~=1
    nbaver=floor(nbaver_init/siz(1)); % number of bursts used for the sliding background,
    if isequal(floor(nbaver/2),nbaver)
        nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined)
    end
    nbaver_init=nbaver*siz(1);%propose by default an integer number of bursts
end

%% create dir of the new images
% [dir_images,namebase]=fileparts(filebase);
if test_level
    term='_b_levels';
else
    term='_b';
end
[pp,subdir_ima]=fileparts(Param.InputTable{1,1});
try
    mkdir([dir_images term]);
catch ME
    msgbox_uvmat('ERROR',ME.message);
    return
end
[xx,msg2] = fileattrib([dir_images term],'+w','g'); %yield writing access (+w) to user group (g)
if ~strcmp(msg2,'')
    msgbox_uvmat('ERROR',['pb of permission for ' subdir_ima term ': ' msg2])%error message for directory creation
    return
end
filebase_b=fullfile([dir_images term],Param.InputTable{1,3});

%% set processing parameters
prompt = {'Number of images for the sliding background (MUST FIT IN COMPUETER MEMORY)';'The number of positions (laser slices)';'volume scan mode (Yes/No)';...
    'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'};
dlg_title = ['get (slice by slice) a sliding background and substract to each image, result in subdir ' subdir_ima term];
num_lines= 3;
def     = { num2str(nbaver_init);num2str(nbslice_i);'No';'0.1'};
answer = inputdlg(prompt,dlg_title,num_lines,def);
set(hseries.ParamVal,'String',answer([1 [3:4]]))
set(hseries.ParamVal,'Visible','on')

nbaver_ima=str2num(answer{1});%number of images for the sliding background
nbaver=ceil(nbaver_ima/siz(1));%number of bursts for the sliding background
if isequal(floor(nbaver/2),nbaver)
    nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined)
end
step=siz(1);%case of bursts: the sliding background is shifted by one burst
vol_test=answer{3};
if isequal(vol_test,'Yes')
    nbfield2=1;%case of volume: no consecutive series at a given level
    nbslice_i=siz(1);%number of slices
else
    nbfield2=siz(1); %nb of consecutive images at each level(burst)
    if siz(2)>1
        % nbslice_i=str2num(answer{2})/(num_i1(1,2)-num_i1(1,1));% number of slices
        nbslice_i=str2num(answer{2})/(i1_series{1}(1,2)-i1_series{1}(1,1));% number of slices
    else
        nbslice_i=1;
    end
    if ~isequal(floor(nbslice_i),nbslice_i)
        msgbox_uvmat('ERROR','the number of slices must be a multiple of the i increment')
        return
    end
end
rank=floor(str2num(answer{4})*nbaver_ima);
if rank==0
    rank=1;%rank selected in the sorted image series
end
lengthtot=siz(1)*siz(2);
nbfield=floor(lengthtot/(nbfield2*nbslice_i));%total number of i indexes (adjusted to an integer number of slices)
nbfield_slice=nbfield*nbfield2;% number of fields per slice
if nbaver_ima > nbfield*nbfield2
    msgbox_uvmat('ERROR','number of images in a slice smaller than the proposed number of images for the sliding average')
    return
end
nbfirst=(ceil(nbaver/2))*step;
if nbfirst>nbaver_ima
    nbfirst=ceil(nbaver_ima/2);
    step=1;
    nbaver=nbaver_ima;
end

%% prealocate memory for the sliding background
% first_image=name_generator(filebase,num_i1(1),num_j1(1),FileExt,NomType);
% Afirst=read_image(first_image,FileType,num_i1(1),MovieObject);
Afirst=read_image(filecell{1,1},FileType,i1_series{1}(1),MovieObject);
[npy,npx]=size(Afirst);
try
    Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
    Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
catch ME
    msgbox_uvmat('ERROR',ME.message)
    return
end

%% copy the xml file
if exist([filebase '.xml'],'file')
    copyfile([filebase '.xml'],[filebase_b '.xml']);% copy the .civ file
    t=xmltree([filebase_b '.xml']);
    
    %update information on the first image name in the series
    uid_Heading=find(t,'ImaDoc/Heading');
    if isempty(uid_Heading)
        [t,uid_Heading]=add(t,1,'element','Heading');
    end
    uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
    if ~isempty(j1_series{1})
        j1=j1_series{1}(1);
    end
    ImageName=fullfile_uvmat([dir_images term],'',Param.InputTable{1,3},'.png',NomType,i1_series{1}(1),[],j1);
    %     ImageName=name_generator(filebase_b,num_i1(1),num_j1(1),'.png',NomType);
    [pth,ImageName]=fileparts(ImageName);
    ImageName=[ImageName '.png'];
    if isempty(uid_ImageName)
        [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
    end
    uid_value=children(t,uid_ImageName);
    if isempty(uid_value)
        t=add(t,uid_ImageName,'chardata',ImageName);%indicate  name of the first image, with ;png extension
    else
        t=set(t,uid_value(1),'value',ImageName);%indicate  name of the first image, with ;png extension
    end
    
    %add information about image transform
    [t,new_uid]=add(t,1,'element','ImageTransform');
    [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction');
    [t]=add(t,NameFunction_uid,'chardata','sub_background');
    if test_level
        [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction');
        [t]=add(t,NameFunction_uid,'chardata','levels');
    end
    [t,NbSlice_uid]=add(t,new_uid,'element','NbSlice');
    [t]=add(t,new_uid,'chardata',num2str(nbslice_i));
    [t,NbSlidingImages_uid]=add(t,new_uid,'element','NbSlidingImages');
    [t]=add(t,NbSlidingImages_uid,'chardata',num2str(nbaver));
    [t,LuminosityRank_uid]=add(t,new_uid,'element','RankBackground');
    [t]=add(t,LuminosityRank_uid,'chardata',num2str(rank));% luminosity rank almong the nbaver sliding images
    save(t,[filebase_b '.xml'])
elseif exist([filebase '.civ'],'file')
    copyfile([filebase '.civ'],[filebase_b '.civ']);% copy the .civ file
end
%copy the mask
if exist([filebase '_1mask_1'],'file')
    copyfile([filebase '_1mask_1'],[filebase_b '_1mask_1']);% copy the mask file
end

%MAIN LOOP ON SLICES

for islice=1:nbslice_i
    %% select the series of image indices at the level islice
    for ifield=1:nbfield
        for iburst=1:nbfield2
            indselect(iburst,ifield)=((ifield-1)*nbslice_i+(islice-1))*nbfield2+iburst;
        end
    end
    
    %% read the first series of nbaver_ima images and sort by luminosity at each pixel
    for ifield = 1:nbaver_ima
        ifile=indselect(ifield);
        filename=filecell{1,ifile};
        % filename=name_generator(filebase,num_i1(ifile),num_j1(ifile),FileExt,NomType);
        Aread=read_image(filename,FileType,i1_series{1}(ifile),MovieObject);
        Ak(:,:,ifield)=Aread;
    end
    Asort=sort(Ak,3);%sort the luminosity of images at each point
    B=Asort(:,:,rank);%background image
    display( 'first background image will be substracted')
    for ifield=1:nbfirst
        Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
        C=uint16(Acor);% set to integer 16 bits
        ifile=indselect(ifield);
        %             newname=name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',NomType)% makes the new file name
        if ~isempty(j1_series{1})
            j1=j1_series{1}(ifile);
        end
        newname=fullfile_uvmat([dir_images term],'',Param.InputTable{1,3},'.png',NomType,i1_series{1}(ifile),[],j1);
        %newname=name_generator(filebase_b,i1_series{1}(ifile),j1_series{1}(ifile),'.png',NomType);% makes the new file name
        if test_level
            C=levels(C);
            imwrite(C,newname,'BitDepth',8); % save the new image
        else
            imwrite(C,newname,'BitDepth',16); % save the new image
        end
    end
    
    %% repeat the operation on a sliding series of nbaver*nbfield2 images
    display('sliding background image will be substracted')
    if nbfield_slice > nbaver_ima
        for ifield = step*ceil(nbaver/2)+1:step:nbfield_slice-step*floor(nbaver/2)
            stopstate=get(hseries.RUN,'BusyAction');
            if isequal(stopstate,'queue')% enable STOP command
                update_waitbar(hseries.waitbar,WaitbarPos,(ifield+(islice-1)*nbfield_slice)/(nbfield_slice*nbslice_i))
                display((ifield+(islice-1)*nbfield_slice)/(nbfield_slice*nbslice_i))
                Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
                %incorporate next burst in the current image series
                for iburst=1:step
                    ifile=indselect(ifield+step*floor(nbaver/2)+iburst-1);
                    filename=name_generator(filebase,num_i1(ifile),num_j1(ifile),FileExt,NomType);
                    Aread=read_image(filename,FileType,num_i1(ifile),MovieObject);
                    Ak(:,:,nbaver_ima-step+iburst)=Aread;
                end
                Asort=sort(Ak,3);%sort the new current image series by luminosity
                B=Asort(:,:,rank);%current background image
                for iburst=1:step
                    index=step*floor(nbaver/2)+iburst;
                    Acor=double(Ak(:,:,index))-double(B);
                    Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
                    C=uint16(Acor);
                    ifile=indselect(ifield+iburst-1);
                    if ~isempty(j1_series{1})
                        j1=j1_series{1}(ifile);
                    end
                    newname=fullfile_uvmat([dir_images term],'',Param.InputTable{1,3},'.png',NomType,i1_series{1}(ifile),[],j1);
                    %[newname]=name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',NomType) % makes the new file name
                    if test_level
                        C=levels(C);
                        imwrite(C,newname,'BitDepth',8); % save the new image
                    else
                        imwrite(C,newname,'BitDepth',16); % save the new image
                    end
                end
            else
                return
            end
        end
    end
    
    %% substract the background from the last images
    display('last background image will be substracted')
    ifield=nbfield_slice-(step*ceil(nbaver/2))+1:nbfield_slice;
    for ifield=nbfield_slice-(step*floor(nbaver/2))+1:nbfield_slice
        index=ifield-nbfield_slice+step*(2*floor(nbaver/2)+1);
        Acor=double(Ak(:,:,index))-double(B);
        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
        C=uint16(Acor);
        ifile=indselect(ifield);
        if ~isempty(j1_series{1})
            j1=j1_series{1}(ifile);
        end
        newname=fullfile_uvmat([dir_images term],'',Param.InputTable{1,3},'.png',NomType,i1_series{1}(ifile),[],j1);
        %newname=name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',NomType);% makes the new file name
        if test_level
            C=levels(C);
            imwrite(C,newname,'BitDepth',8); % save the new image
        else
            imwrite(C,newname,'BitDepth',16); % save the new image
        end
    end
end

%finish the waitbar
update_waitbar(hseries.waitbar,WaitbarPos,1)


%------------------------------------------------------------------------
%--read images and convert them to the uint16 format used for PIV
function A=read_image(filename,type_ima,num,MovieObject)
%------------------------------------------------------------------------
%num is the view number needed for an avi movie
switch type_ima
    case 'movie'
        A=read(MovieObject,num);
    case 'avi'
        mov=aviread(filename,num);
        A=frame2im(mov(1));
    case 'multimage'
        A=imread(filename,num);
    case 'image'    
        A=imread(filename);
end
siz=size(A);
if length(siz)==3;%color images
    A=sum(double(A),3);
end
    

function C=levels(A)
%whos A;
B=double(A(:,:,1));
windowsize=round(min(size(B,1),size(B,2))/20);
windowsize=floor(windowsize/2)*2+1;
ix=1/2-windowsize/2:-1/2+windowsize/2;%
%del=np/3;
%fct=exp(-(ix/del).^2);
fct2=cos(ix/(windowsize-1)/2*pi/2);
%Mfiltre=(ones(5,5)/5^2);
%Mfiltre=fct2';
Mfiltre=fct2'*fct2;
Mfiltre=Mfiltre/(sum(sum(Mfiltre)));

C=filter2(Mfiltre,B);
C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
C=tanh(B./(2*C));
[n,c]=hist(reshape(C,1,[]),100);
% figure;plot(c,n);

[m,i]=max(n);
c_max=c(i);
[dummy,index]=sort(abs(c-c(i)));
n=n(index);
c=c(index);
i_select = find(cumsum(n)<0.95*sum(n));
if isempty(i_select)
    i_select = 1:length(c);
end
c_select=c(i_select);
n_select=n(i_select);
cmin=min(c_select);
cmax=max(c_select);
C=(C-cmin)/(cmax-cmin)*256;
C=uint8(C);