source: trunk/src/series/sub_background.m @ 1126

Last change on this file since 1126 was 1126, checked in by g7moreau, 6 months ago

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[457]1%'sub_background': substract a sliding background to an image series
[169]2%------------------------------------------------------------------------
[24]3% Method:
4    %calculate the background image by sorting the luminosity of each point
5    % over a sliding sub-sequence of 'nbaver_ima' images.
6    % The luminosity value of rank 'rank' is selected as the
7    % 'background'. rank=nbimages/2 gives the median value.  Smaller values are appropriate
8    % for a dense set of particles. The extrem value rank=1 gives the true minimum
9    % luminosity, but it can be polluted by noise.
10% Organization of image indices:
[454]11    % The program is working on a series of images,
12    % In the mode 'volume', nbfield2=1 (1 image at each level)and NbSlice (=nbfield_j)
13    % Else nbfield2=nbfield_j =nbre of images in a burst (j index)
[451]14   
[457]15% function GUI_config=sub_background(Param)
[169]16%
[451]17%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
[457]18%
[451]19%OUTPUT
[596]20% ParamOut: sets options in the GUI series.fig needed for the function
[451]21%
22%INPUT:
23% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
24% In batch mode, Param is the name of the corresponding xml file containing the same information
[596]25% when Param.Action.RUN=0 (as activated when the current Action is selected
26% in series), the function ouput paramOut set the activation of the needed GUI elements
[451]27%
[596]28% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
29% see the current structure Param)
[451]30%    .InputTable: cell of input file names, (several lines for multiple input)
31%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
32%    .OutputSubDir: name of the subdirectory for data outputs
[596]33%    .OutputDirExt: directory extension for data outputs
[451]34%    .Action: .ActionName: name of the current activated function
35%             .ActionPath:   path of the current activated function
[596]36%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
37%             .RUN =0 for GUI input, =1 for function activation
38%             .RunMode='local','background', 'cluster': type of function  use
39%             
[451]40%    .IndexRange: set the file or frame indices on which the action must be performed
41%    .FieldTransform: .TransformName: name of the selected transform function
42%                     .TransformPath:   path  of the selected transform function
43%    .InputFields: sub structure describing the input fields withfields
[596]44%              .FieldName: name(s) of the field
[451]45%              .VelType: velocity type
46%              .FieldName_1: name of the second field in case of two input series
47%              .VelType_1: velocity type of the second field in case of two input series
[596]48%              .Coord_y: name of y coordinate variable
49%              .Coord_x: name of x coordinate variable
[451]50%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
51%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[810]52
53%=======================================================================
[1126]54% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
[810]55%   http://www.legi.grenoble-inp.fr
56%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
57%
58%     This file is part of the toolbox UVMAT.
59%
60%     UVMAT is free software; you can redistribute it and/or modify
61%     it under the terms of the GNU General Public License as published
62%     by the Free Software Foundation; either version 2 of the license,
63%     or (at your option) any later version.
64%
65%     UVMAT is distributed in the hope that it will be useful,
66%     but WITHOUT ANY WARRANTY; without even the implied warranty of
67%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
68%     GNU General Public License (see LICENSE.txt) for more details.
69%=======================================================================
70
[459]71function ParamOut=sub_background (Param)
[24]72
[676]73%%%%%%%%%%%%%%%%%    INPUT PREPARATION MODE (no RUN)    %%%%%%%%%%%%%%%%%
[592]74if isstruct(Param) && isequal(Param.Action.RUN,0)
[605]75    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
76    ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
[897]77    ParamOut.NbSlice='on'; % edit box nbre of slices made active
[605]78    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
79    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
80    ParamOut.FieldTransform = 'off';%can use a transform function
81    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
82    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
[592]83    ParamOut.OutputDirExt='.sback';%set the output dir extension
[605]84    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
[592]85   
86    %% root input file(s) and type
[716]87    % check the existence of the first file in the series
[917]88        first_j=[];% note that the function will propose to cover the whole range of indices
89    if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end
[716]90    last_j=[];
[917]91    if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end
[716]92    PairString='';
93    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
94    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
95    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
96        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
97    if ~exist(FirstFileName,'file')
98        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
99    else
100        [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
101        LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
102        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
103        if ~exist(FirstFileName,'file')
104             msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
105        end
[605]106    end
[716]107
[592]108    %% check the validity of  input file types
[784]109    FileInfo=get_file_info(FirstFileName);
[783]110    FileType=FileInfo.FileType;
[1033]111    CheckImage=strcmp(FileInfo.FieldType,'image');% =1 for images
[592]112    if ~CheckImage
[642]113        msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not an image'])
[451]114        return
[592]115    end
116   
[676]117    %% numbers of fields
[897]118    NbSlice_i=1;%default
[676]119    if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
[897]120        NbSlice_i=Param.IndexRange.NbSlice;
[592]121    end
[774]122    incr_j=1;%default
123    if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j)
124        incr_j=Param.IndexRange.incr_j;
125    end
126    if isempty(first_j)||isempty(last_j)
127        nbfield_j=1;
128    else
129        nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices)
130    end
[897]131    first_i=1;last_i=1;incr_i=1;%default
[917]132    if isfield(Param.IndexRange,'MinIndex_i'); first_i=Param.IndexRange.MinIndex_i; end   
133    if isfield(Param.IndexRange,'MaxIndex_i'); last_i=Param.IndexRange.MaxIndex_i; end
[774]134    if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i)
135        incr_i=Param.IndexRange.incr_i;
136    end
137    nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices)
[676]138    nbfield=nbfield_j*nbfield_i; %total number of fields
[897]139    nbfield_i=floor(nbfield/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
[592]140   
[676]141    %% setting of  parameters specific to sub_background
[1058]142    CheckVolume='No';
143    nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts
[1124]144    SaturationValue=0;
145     if nbfield_i~=1 && nbfield_j<=nbaver_init
[592]146        nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background,
[854]147        if isequal(mod(nbaver,2),0)% if nbaver is even
[592]148            nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined)
149        end
150        nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts
151    end
[1058]152    BrightnessRankThreshold=0.1;
[1124]153   % CheckSubmedian='No';
154%     SaturationCoeff=0;
[1058]155    if isfield(Param,'ActionInput')
156        if isfield(Param.ActionInput,'CheckVolume') && Param.ActionInput.CheckVolume
157            CheckVolume='Yes';
158        end
159        if isfield(Param.ActionInput,'SlidingSequenceLength')
160         nbaver_init=Param.ActionInput.SlidingSequenceLength;
161        end
162        if isfield(Param.ActionInput,'BrightnessRankThreshold')
163          BrightnessRankThreshold=Param.ActionInput.BrightnessRankThreshold;
164        end
[1124]165%         if isfield(Param.ActionInput,'CheckSubmedian') && Param.ActionInput.CheckSubmedian
166%         CheckSubmedian='Yes';
167%         end
168        if isfield(Param.ActionInput,'SaturationValue')
169            SaturationValue=Param.ActionInput.SaturationValue;
[1058]170        end
171    end   
[951]172    prompt = {'volume scan mode (Yes/No)';...
173        'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';...
174        'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles';...
[1124]175        'image saturation level for rescaling( reduce the influence of particles brighter than this value), =0 for no rescaling' };
[676]176    dlg_title = 'get (slice by slice) a sliding background and substract to each image';
[1124]177    num_lines= 4;
178    def     = { CheckVolume;num2str(nbaver_init);num2str(BrightnessRankThreshold);num2str(SaturationValue)};
[676]179    answer = inputdlg(prompt,dlg_title,num_lines,def);
[917]180    if isempty(answer)
181        return
182    end
[676]183    %check input consistency
[897]184    if strcmp(answer{1},'No') && ~isequal(NbSlice_i,1)
185        check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice_i) ' slices']);
[676]186        if ~strcmp(check,'Yes')
187            return
[592]188        end
189    end
[676]190    if strcmp(answer{1},'Yes')
[1124]191        step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume
[897]192        ParamOut.NbSlice=1; %nbre of slices displayed
[676]193    else
194        step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
195    end
[1124]196    ParamOut.ActionInput.SlidingSequenceLength=adjust_slidinglength(str2num(answer{2}),step);
[599]197    ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes');
[854]198    ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3});
[1124]199%     ParamOut.ActionInput.CheckSubmedian=strcmp(answer{4},'Yes');
200    ParamOut.ActionInput.SaturationValue=str2double(answer{4});
[592]201    % apply the image rescaling function 'level' (avoid the blinking effects of bright particles)
[951]202%     answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background');
203%     ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes');
[592]204    return
[24]205end
[676]206%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%%
[24]207
[592]208%% read input parameters from an xml file if input is a file name (batch mode)
209checkrun=1;
[904]210RUNHandle=[];
211WaitbarHandle=[];
[457]212if ischar(Param)
[592]213    Param=xml2struct(Param);% read Param as input file (batch case)
214    checkrun=0;
[904]215else
[624]216hseries=findobj(allchild(0),'Tag','series');
217RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
218WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
[904]219end
[676]220
221%% input preparation
[897]222NbSlice_i=Param.IndexRange.NbSlice;
223if ~isequal(NbSlice_i,1)
224    display(['multi-level splitting into ' num2str(NbSlice_i) ' slices']);
[592]225end
[457]226RootPath=Param.InputTable(:,1);
227RootFile=Param.InputTable(:,3);
228SubDir=Param.InputTable(:,2);
229NomType=Param.InputTable(:,4);
230FileExt=Param.InputTable(:,5);
[897]231%hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
232[filecell,i1_series,i2_series,j1_series]=get_file_series(Param);
233% if ~isempty(hdisp),delete(hdisp),end;
[676]234%%%%%%%%%%%%
235    % The cell array filecell is the list of input file names, while
236    % filecell{iview,fileindex}:
237    %        iview: line in the table corresponding to a given file series
238    %        fileindex: file index within  the file series,
239    % 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
240    % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
241%%%%%%%%%%%%
[784]242[FileInfo{1},MovieObject{1}]=get_file_info(filecell{1,1});
[783]243FileType{1}=FileInfo{1}.FileType;
[592]244    if ~isempty(j1_series{1})
245        frame_index{1}=j1_series{1};
246    else
247        frame_index{1}=i1_series{1};
248    end
[451]249
[897]250
251%% output file naming
[951]252FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image'
253if strcmp(FileInfo{1}.FileType,'image')
254    NomTypeOut=NomType{1};
[802]255elseif isempty(j1_series{1})
[592]256    NomTypeOut='_1';
[454]257else
[592]258    NomTypeOut='_1_1';% caseof purely numerical indexing
[454]259end
[592]260OutputDir=[Param.OutputSubDir Param.OutputDirExt];
[1124]261OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
[451]262
[897]263%% file index parameters
[1124]264% NbSlice_i: nbre of slices for i index in multi-level mode: equal to 1 for a single level
[897]265% the function sub_background is then relaunched by the GUI series for each
266%      slice, incrementing the first index i by 1
267% NbSlice_j: nbre of slices in volume mode
268% nbfield : total number of images treated per slice
269% step: shift of image index at each step of the sliding background (corresponding to the nbre of images in a burst)
270% nbaver_ima: nbre of the images in the sliding sequence used for the background
271% nbaver=nbaver_ima/step: nbre of bursts corresponding to nbaver_ima images. It has been adjusted so that nbaver is an odd integer
272nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
273nbfield_i=size(i1_series{1},2); %nb of fields for the i index
[917]274
[1124]275if Param.ActionInput.CheckVolume% case of volume scan: the background images must be determined for each index j
[897]276    step=2;% we assume the burst contains only one image pair
277    NbSlice_j=nbfield_j;
278    nbfield_series=nbfield_i;
279else
[592]280    step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
[1124]281    NbSlice_j=1;
[917]282    %nbfield_i=floor(nbfield_i/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
283    %nbfield=nbfield_i*NbSlice_i; %total number of fields after adjustement
284    nbfield_series=nbfield_i*nbfield_j;
[54]285end
[917]286nbfield=nbfield_j*nbfield_i; %total number of fields
[1124]287[nbaver_ima,nbaver,step]=adjust_slidinglength(Param.ActionInput.SlidingSequenceLength,step);
[592]288if nbaver_ima > nbfield
289    display('number of images in a slice smaller than the proposed number of images for the sliding average')
290    return
[24]291end
[897]292halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background
[454]293
[897]294%% calculate absolute brightness rank
[599]295rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima);
[24]296if rank==0
297    rank=1;%rank selected in the sorted image series
298end
299
[239]300%% prealocate memory for the sliding background
[394]301try
[454]302    Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1));
[700]303    [npy,npx,nbcolor]=size(Afirst);% the argument nbcolor is important to get npx right for color images
[454]304    if strcmp(class(Afirst),'uint8') % case of 8bit images
305        Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
306        Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
307    else
308        Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
309        Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
310    end
[239]311catch ME
[592]312    msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message])
[239]313    return
314end
315
[24]316
[897]317%%%%%%%  LOOP ON SLICES FOR VOLUME SCAN %%%%%%%
318for j_slice=1:NbSlice_j
319    %% select the series of i indices to process
320    indselect=j_slice:step*NbSlice_j:nbfield;% select file indices of the slice
321    for ifield=1:step-1
322        indselect=[indselect;indselect(end,:)+NbSlice_j];
[394]323    end
[214]324   
[897]325    %% read the first series of nbaver_ima images and sort by luminosity at each pixel
326    for ifield = 1:nbaver_ima
327        ifile=indselect(ifield);
328        filename=filecell{1,ifile};
329        Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
[1124]330        if ndims(Aread)==3%color images
[897]331            Aread=sum(double(Aread),3);% take the sum of color components
[454]332        end
[897]333        Ak(:,:,ifield)=Aread;
[24]334    end
[897]335    Asort=sort(Ak,3);%sort the luminosity of images at each point
336    B=Asort(:,:,rank);%background image
337   
338    %% substract the first background image to the first images
339    display( 'first background image will be substracted')
[1124]340    for ifield=1:step*(halfnbaver+1)% nbre of images treated by the first background image
[897]341        Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
342        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
343        ifile=indselect(ifield);
344        j1=1;
345        if ~isempty(j1_series{1})
346            j1=j1_series{1}(ifile);
[676]347        end
[1124]348        newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
[897]349       
350        %write result file
[1124]351        if ~isequal(Param.ActionInput.SaturationValue,0)
352            C=levels(Acor,Param.ActionInput.SaturationValue);
[950]353            imwrite(C,newname,'BitDepth',16); % save the new image
[897]354        else
[1032]355            if ~isfield(FileInfo{1},'BitDepth')
356                FileInfo{1}.BitDepth=16;
357            end
[897]358            if isequal(FileInfo{1}.BitDepth,16)
359                C=uint16(Acor);
360                imwrite(C,newname,'BitDepth',16); % save the new image
361            else
362                C=uint8(Acor);
363                imwrite(C,newname,'BitDepth',8); % save the new image
[442]364            end
[676]365        end
[897]366        display([newname ' written'])
367    end
368   
369    %% repeat the operation on a sliding series of images
370    display('sliding background image will be substracted')
371    if nbfield_series > nbaver_ima
372        for ifield = step*(halfnbaver+1):step:nbfield_series-step*(halfnbaver+1)% ifield +iburst=index of the current processed image
373            update_waitbar(WaitbarHandle,ifield/nbfield_series)
[904]374            if  ~isempty(RUNHandle)&&~strcmp(get(RUNHandle,'BusyAction'),'queue')
[897]375                disp('program stopped by user')
376                return
[676]377            end
[897]378            if nbaver_ima>step
379            Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
380            end
381            %incorporate next burst in the current image series
382            for iburst=1:step
383                ifile=indselect(ifield+iburst+step*halfnbaver);
384                j1=1;
385                if ~isempty(j1_series{1})
386                    j1=j1_series{1}(ifile);
387                end
[1124]388               
[897]389                filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
[1032]390                Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
[1124]391                if ndims(Aread)==3%case of color images
[897]392                    Aread=sum(double(Aread),3);% take the sum of color components
393                end
394                Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image
395            end
396            Asort=sort(Ak,3);%sort the new current image series by luminosity
397            B=Asort(:,:,rank);%current background image
398            %substract the background for the current burst
399            for iburst=1:step
400                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
401                Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
402                ifile=indselect(ifield+iburst);
403                if ~isempty(j1_series{1})
404                    j1=j1_series{1}(ifile);
405                end
[1124]406                newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
[897]407                %write result file
[1124]408                if ~isequal(Param.ActionInput.SaturationValue,0)
409                    C=levels(Acor,Param.ActionInput.SaturationValue);
[950]410                    imwrite(C,newname,'BitDepth',16); % save the new image
[676]411                else
[897]412                    if isequal(FileInfo{1}.BitDepth,16)
413                        C=uint16(Acor);
414                        imwrite(C,newname,'BitDepth',16); % save the new image
415                    else
416                        C=uint8(Acor);
417                        imwrite(C,newname,'BitDepth',8); % save the new image
418                    end
[214]419                end
[897]420                display([newname ' written'])
[24]421            end
[676]422        end
[24]423    end
[897]424   
425    %% substract the background from the last images
426    display('last background image will be substracted')
427    for  ifield=nbfield_series-step*halfnbaver+1:nbfield_series
428        Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B);
429        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
430        ifile=indselect(ifield);
431        if ~isempty(j1_series{1})
432            j1=j1_series{1}(ifile);
433        end
[1124]434        newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
[897]435        %write result file
[1124]436        if ~isequal(Param.ActionInput.SaturationValue,0)
437            C=levels(Acor,Param.ActionInput.SaturationValue);
[950]438            imwrite(C,newname,'BitDepth',16); % save the new image
[616]439        else
[897]440            if isequal(FileInfo{1}.BitDepth,16)
441                C=uint16(Acor);
442                imwrite(C,newname,'BitDepth',16); % save the new image
443            else
444                C=uint8(Acor);
445                imwrite(C,newname,'BitDepth',8); % save the new image
446            end
[394]447        end
[897]448        display([newname ' written'])
[394]449    end
[24]450end
451
[1124]452function C=levels(A,Coeff)
[214]453
[1124]454% nblock_y=100;%2*Param.TransformInput.BlockSize;
455% nblock_x=100;%2*Param.TransformInput.BlockSize;
456% [npy,npx]=size(A);
457% [X,Y]=meshgrid(1:npx,1:npy);
458%
459% %Backg=zeros(size(A));
460% %Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
461% %Amin=A.*Aflagmin;%values of A at local minima
462% % local background: find all the local minima in image subblocks
463% if CheckSubmedian
464%     fctblock= inline('median(x(:))');
465%     Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in  blocks
466%     %B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
467%     A=A-imresize(Backg,size(A),'bilinear');% substract background interpolated to the initial size image
468% end
469% fctblock= inline('mean(x(:))');
470% AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
471% fctblock= inline('var(x(:))');
472% AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
473% Avalue=AVar./AMean;% typical value of particle luminosity
474% Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image
475%C=uint16(1000*tanh(A./(Coeff*Avalue)));
476C=uint16(Coeff*tanh(A./Coeff));
477%------------------------------------------
478% adjust the number of images used for the sliding average
479function [nbaver_ima,nbaver,step_out]=adjust_slidinglength(nb_aver_in,step)
480%nbaver_ima=str2double(nb_aver_in);%number of images for the sliding background
481nbaver=ceil(nb_aver_in/step);%number of bursts for the sliding background
482if isequal(mod(nbaver,2),0)% if nbaver is even
483    nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
[951]484end
[1124]485step_out=step;
486if nbaver>1
487    nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver
488else
489    nbaver_ima=nb_aver_in;
490    if isequal(mod(nbaver_ima,2),0)% if nbaver_ima is even
491        nbaver_ima=nbaver_ima+1;%set the number of bursts to an odd number (so the middle burst is defined)
492    end
493    step_out=1;
494end
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