source: trunk/src/series/sub_background.m @ 1175

Last change on this file since 1175 was 1175, checked in by sommeria, 4 days ago

add loglin histogram in uvmat and image rescale in civ_series

File size: 24.0 KB
Line 
1%'sub_background': substract a sliding background to an image series
2%------------------------------------------------------------------------
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:
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)
14   
15% function GUI_config=sub_background(Param)
16%
17%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
18%
19%OUTPUT
20% ParamOut: sets options in the GUI series.fig needed for the function
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
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
27%
28% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
29% see the current structure Param)
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
33%    .OutputDirExt: directory extension for data outputs
34%    .Action: .ActionName: name of the current activated function
35%             .ActionPath:   path of the current activated function
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%             
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
44%              .FieldName: name(s) of the field
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
48%              .Coord_y: name of y coordinate variable
49%              .Coord_x: name of x coordinate variable
50%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
51%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
52
53%=======================================================================
54% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
55%   http://www.legi.grenoble-inp.fr
56%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.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
71function ParamOut=sub_background (Param)
72
73%%%%%%%%%%%%%%%%%    INPUT PREPARATION MODE (no RUN)    %%%%%%%%%%%%%%%%%
74if isstruct(Param) && isequal(Param.Action.RUN,0)
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)
77    ParamOut.NbSlice='on'; % edit box nbre of slices made active
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';%cannot use projection object(option 'off'/'on',
82    ParamOut.Mask='on';%can use mask option   (option 'off'/'on', 'off' by default)
83    ParamOut.OutputDirExt='.sback';%set the output dir extension
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
85   
86    %% root input file(s) and type
87    % check the existence of the first file in the series
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
90    last_j=[];
91    if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end
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
106    end
107
108    %% check the validity of  input file types
109    FileInfo=get_file_info(FirstFileName);
110    FileType=FileInfo.FileType;
111    CheckImage=strcmp(FileInfo.FieldType,'image');% =1 for images
112    if ~CheckImage
113        msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not an image'])
114        return
115    end
116   
117    %% numbers of fields
118    NbSlice_i=1;%default
119    if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
120        NbSlice_i=Param.IndexRange.NbSlice;
121    end
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
131    first_i=1;last_i=1;incr_i=1;%default
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
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)
138    nbfield=nbfield_j*nbfield_i; %total number of fields
139    nbfield_i=floor(nbfield/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
140   
141    %% setting of  parameters specific to sub_background
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
144    SaturationValue=0;
145     if nbfield_i~=1 && nbfield_j<=nbaver_init
146        nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background,
147        if isequal(mod(nbaver,2),0)% if nbaver is even
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
152    BrightnessRankThreshold=0.1;
153    if isfield(Param,'ActionInput')
154        if isfield(Param.ActionInput,'CheckVolume') && Param.ActionInput.CheckVolume
155            CheckVolume='Yes';
156        end
157        if isfield(Param.ActionInput,'SlidingSequenceLength')
158         nbaver_init=Param.ActionInput.SlidingSequenceLength;
159        end
160        if isfield(Param.ActionInput,'BrightnessRankThreshold')
161          BrightnessRankThreshold=Param.ActionInput.BrightnessRankThreshold;
162        end
163%         if isfield(Param.ActionInput,'CheckSubmedian') && Param.ActionInput.CheckSubmedian
164%         CheckSubmedian='Yes';
165%         end
166        if isfield(Param.ActionInput,'SaturationValue')
167            SaturationValue=Param.ActionInput.SaturationValue;
168        end
169    end   
170    prompt = {'volume scan mode (Yes/No)';...
171        'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';...
172        'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles';...
173        'image saturation level for rescaling( reduce the influence of particles brighter than this value), =0 for no rescaling' };
174    dlg_title = 'get (slice by slice) a sliding background and substract to each image';
175    num_lines= 4;
176    def     = { CheckVolume;num2str(nbaver_init);num2str(BrightnessRankThreshold);num2str(SaturationValue)};
177    answer = inputdlg(prompt,dlg_title,num_lines,def);
178    if isempty(answer)
179        return
180    end
181    %check input consistency
182    if strcmp(answer{1},'No') && ~isequal(NbSlice_i,1)
183        check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice_i) ' slices']);
184        if ~strcmp(check,'Yes')
185            return
186        end
187    end
188    if strcmp(answer{1},'Yes')
189        step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume
190        ParamOut.NbSlice=1; %nbre of slices displayed
191    else
192        step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
193    end
194    ParamOut.ActionInput.SlidingSequenceLength=adjust_slidinglength(str2num(answer{2}),step);
195    ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes');
196    ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3});
197%     ParamOut.ActionInput.CheckSubmedian=strcmp(answer{4},'Yes');
198    ParamOut.ActionInput.SaturationValue=str2double(answer{4});
199    % apply the image rescaling function 'level' (avoid the blinking effects of bright particles)
200%     answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background');
201%     ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes');
202    return
203end
204%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%%
205
206%% read input parameters from an xml file if input is a file name (batch mode)
207checkrun=1;
208RUNHandle=[];
209WaitbarHandle=[];
210if ischar(Param)
211    Param=xml2struct(Param);% read Param as input file (batch case)
212    checkrun=0;
213else
214hseries=findobj(allchild(0),'Tag','series');
215RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
216WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
217end
218
219%% input preparation
220NbSlice_i=Param.IndexRange.NbSlice;
221if ~isequal(NbSlice_i,1)
222    display(['multi-level splitting into ' num2str(NbSlice_i) ' slices']);
223end
224RootPath=Param.InputTable(:,1);
225RootFile=Param.InputTable(:,3);
226SubDir=Param.InputTable(:,2);
227NomType=Param.InputTable(:,4);
228FileExt=Param.InputTable(:,5);
229[filecell,i1_series,i2_series,j1_series]=get_file_series(Param);%series of file names organised as a single array
230
231%%%%%%%%%%%%
232    % The cell array filecell is the list of input file names, while
233    % filecell{iview,fileindex}:
234    %        iview: line in the table corresponding to a given file series
235    %        fileindex: file index within  the file series,
236    % 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
237    % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
238%%%%%%%%%%%%
239[FileInfo{1},MovieObject{1}]=get_file_info(filecell{1,1});
240FileType{1}=FileInfo{1}.FileType;
241    if ~isempty(j1_series{1})
242        frame_index{1}=j1_series{1};
243    else
244        frame_index{1}=i1_series{1};
245    end
246
247
248%% output file naming
249FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image'
250if strcmp(FileInfo{1}.FileType,'image')
251    NomTypeOut=NomType{1};
252elseif isempty(j1_series{1})
253    NomTypeOut='_1';
254else
255    NomTypeOut='_1_1';% caseof purely numerical indexing
256end
257OutputDir=[Param.OutputSubDir Param.OutputDirExt];
258OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
259
260%% file index parameters
261% NbSlice_i: nbre of slices for i index in multi-level mode: equal to 1 for a single level
262% the function sub_background is then relaunched by the GUI series for each
263%      slice, incrementing the first index i by 1
264% NbSlice_j: nbre of slices in volume mode
265% nbfield : total number of images treated per slice
266% step: shift of image index at each step of the sliding background (corresponding to the nbre of images in a burst)
267% nbaver_ima: nbre of the images in the sliding sequence used for the background
268% nbaver=nbaver_ima/step: nbre of bursts corresponding to nbaver_ima images. It has been adjusted so that nbaver is an odd integer
269nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
270nbfield_i=size(i1_series{1},2); %nb of fields for the i index
271
272if Param.ActionInput.CheckVolume% case of volume scan: the background images must be determined for each index j
273    step=2;% we assume the burst contains only one image pair
274    NbSlice_j=nbfield_j;
275    nbfield_series=nbfield_i;
276else
277    step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
278    NbSlice_j=1;
279    nbfield_series=nbfield_i*nbfield_j;
280end
281nbfield=nbfield_j*nbfield_i; %total number of fields
282[nbaver_ima,nbaver,step]=adjust_slidinglength(Param.ActionInput.SlidingSequenceLength,step);
283if nbaver_ima > nbfield
284    display('number of images in a slice smaller than the proposed number of images for the sliding average')
285    return
286end
287halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background
288
289%% calculate absolute brightness rank
290rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima);
291if rank==0
292    rank=1;%rank selected in the sorted image series
293end
294
295%% prealocate memory for the sliding background
296try
297    Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1));
298    [npy,npx,nbcolor]=size(Afirst);% the argument nbcolor is important to get npx right for color images
299    if strcmp(class(Afirst),'uint8') % case of 8bit images
300        Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
301        Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
302    else
303        Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
304        Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
305    end
306catch ME
307    msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message])
308    return
309end
310
311%selection of frame indices
312if Param.ActionInput.CheckVolume
313    nbfield=floor(nbfield/NbSlice_j)*NbSlice_j;% truncate the total number of frames in case of incomplete series
314    indselect=1:nbfield;
315     indselect=reshape(indselect,NbSlice_j,[]);
316      NbSlice=NbSlice_j;
317else
318       NbSlice=NbSlice_i;
319    nbfield=floor(nbfield/NbSlice)*NbSlice;% truncate the total number of frames in case of incomplete series
320    indselect=reshape(1:nbfield,NbSlice,[]);
321    for j_slice=1:NbSlice
322    indselect(j_slice,:)=j_slice:step*NbSlice:nbfield;% select file indices of the slice
323    end
324end
325
326%%%%%%%  LOOP ON SLICES %%%%%%%
327for j_slice=1:NbSlice
328    %% select the series of i indices to process
329 %   indselect=j_slice:step*NbSlice_j:nbfield;% select file indices of the slice
330%     for ifield=1:step-1
331%         indselect=[indselect;indselect(end,:)+NbSlice];
332%     end
333   
334    %% read the first series of nbaver_ima images and sort by luminosity at each pixel
335    for ifield = 1:nbaver_ima
336        ifile=indselect(jslice,ifield);
337        filename=filecell{1,ifile};
338        Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
339        if ndims(Aread)==3%color images
340            Aread=sum(double(Aread),3);% take the sum of color components
341        end
342        Ak(:,:,ifield)=Aread;
343    end
344    Asort=sort(Ak,3);%sort the luminosity of images at each point
345    B=Asort(:,:,rank);%background image
346   
347    %% substract the first background image to the first images
348    display( 'first background image will be substracted')
349    for ifield=1:step*(halfnbaver+1)% nbre of images treated by the first background image
350        Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
351        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
352        ifile=indselect(jslice,ifield);
353        j1=1;
354        if ~isempty(j1_series{1})
355            j1=j1_series{1}(ifile);
356        end
357        newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
358       
359        %write result file
360        if ~isequal(Param.ActionInput.SaturationValue,0)
361            C=levels(Acor,Param.ActionInput.SaturationValue);
362            imwrite(C,newname,'BitDepth',16); % save the new image
363        else
364            if ~isfield(FileInfo{1},'BitDepth')
365                FileInfo{1}.BitDepth=16;
366            end
367            if isequal(FileInfo{1}.BitDepth,16)
368                C=uint16(Acor);
369                imwrite(C,newname,'BitDepth',16); % save the new image
370            else
371                C=uint8(Acor);
372                imwrite(C,newname,'BitDepth',8); % save the new image
373            end
374        end
375        display([newname ' written'])
376    end
377   
378    %% repeat the operation on a sliding series of images
379    display('sliding background image will be substracted')
380    if nbfield_series > nbaver_ima
381        for ifield = step*(halfnbaver+1):step:nbfield_series-step*(halfnbaver+1)% ifield +iburst=index of the current processed image
382            update_waitbar(WaitbarHandle,ifield/nbfield_series)
383            if  ~isempty(RUNHandle)&&~strcmp(get(RUNHandle,'BusyAction'),'queue')
384                disp('program stopped by user')
385                return
386            end
387            if nbaver_ima>step
388            Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
389            end
390            %incorporate next burst in the current image series
391            for iburst=1:step
392                ifile=indselect(jslice,ifield+iburst+step*halfnbaver);
393                j1=1;
394                if ~isempty(j1_series{1})
395                    j1=j1_series{1}(ifile);
396                end
397               
398                filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
399                Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
400                if ndims(Aread)==3%case of color images
401                    Aread=sum(double(Aread),3);% take the sum of color components
402                end
403                Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image
404            end
405            Asort=sort(Ak,3);%sort the new current image series by luminosity
406            B=Asort(:,:,rank);%current background image
407            %substract the background for the current burst
408            for iburst=1:step
409                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
410                Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
411                ifile=indselect(jslice,ifield+iburst);
412                if ~isempty(j1_series{1})
413                    j1=j1_series{1}(ifile);
414                end
415                newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
416                %write result file
417                if ~isequal(Param.ActionInput.SaturationValue,0)
418                    C=levels(Acor,Param.ActionInput.SaturationValue);
419                    imwrite(C,newname,'BitDepth',16); % save the new image
420                else
421                    if isequal(FileInfo{1}.BitDepth,16)
422                        C=uint16(Acor);
423                        imwrite(C,newname,'BitDepth',16); % save the new image
424                    else
425                        C=uint8(Acor);
426                        imwrite(C,newname,'BitDepth',8); % save the new image
427                    end
428                end
429                display([newname ' written'])
430            end
431        end
432    end
433   
434    %% substract the background from the last images
435    display('last background image will be substracted')
436    for  ifield=nbfield_series-step*halfnbaver+1:nbfield_series
437        Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B);
438        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
439        ifile=indselect(jslice,ifield);
440        if ~isempty(j1_series{1})
441            j1=j1_series{1}(ifile);
442        end
443        newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
444        %write result file
445        if ~isequal(Param.ActionInput.SaturationValue,0)
446            C=levels(Acor,Param.ActionInput.SaturationValue);
447            imwrite(C,newname,'BitDepth',16); % save the new image
448        else
449            if isequal(FileInfo{1}.BitDepth,16)
450                C=uint16(Acor);
451                imwrite(C,newname,'BitDepth',16); % save the new image
452            else
453                C=uint8(Acor);
454                imwrite(C,newname,'BitDepth',8); % save the new image
455            end
456        end
457        display([newname ' written'])
458    end
459end
460
461function C=levels(A,Coeff)
462
463% nblock_y=100;%2*Param.TransformInput.BlockSize;
464% nblock_x=100;%2*Param.TransformInput.BlockSize;
465% [npy,npx]=size(A);
466% [X,Y]=meshgrid(1:npx,1:npy);
467%
468% %Backg=zeros(size(A));
469% %Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
470% %Amin=A.*Aflagmin;%values of A at local minima
471% % local background: find all the local minima in image subblocks
472% if CheckSubmedian
473%     fctblock= inline('median(x(:))');
474%     Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in  blocks
475%     %B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
476%     A=A-imresize(Backg,size(A),'bilinear');% substract background interpolated to the initial size image
477% end
478% fctblock= inline('mean(x(:))');
479% AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
480% fctblock= inline('var(x(:))');
481% AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
482% Avalue=AVar./AMean;% typical value of particle luminosity
483% Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image
484%C=uint16(1000*tanh(A./(Coeff*Avalue)));
485C=uint16(Coeff*tanh(A./Coeff));
486%------------------------------------------
487% adjust the number of images used for the sliding average
488function [nbaver_ima,nbaver,step_out]=adjust_slidinglength(nb_aver_in,step)
489%nbaver_ima=str2double(nb_aver_in);%number of images for the sliding background
490nbaver=ceil(nb_aver_in/step);%number of bursts for the sliding background
491if isequal(mod(nbaver,2),0)% if nbaver is even
492    nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
493end
494step_out=step;
495if nbaver>1
496    nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver
497else
498    nbaver_ima=nb_aver_in;
499    if isequal(mod(nbaver_ima,2),0)% if nbaver_ima is even
500        nbaver_ima=nbaver_ima+1;%set the number of bursts to an odd number (so the middle burst is defined)
501    end
502    step_out=1;
503end
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