source: trunk/src/series/sub_background.m @ 1061

Last change on this file since 1061 was 1061, checked in by g7moreau, 2 years ago
  • Update copyright to year 2019
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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 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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
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';%can use projection object(option 'off'/'on',
82    ParamOut.Mask='off';%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     if nbfield_i~=1
145        nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background,
146        if isequal(mod(nbaver,2),0)% if nbaver is even
147            nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined)
148        end
149        nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts
150    end
151    BrightnessRankThreshold=0.1;
152    CheckSubmedian='No';
153    SaturationCoeff=0;
154    if isfield(Param,'ActionInput')
155        if isfield(Param.ActionInput,'CheckVolume') && Param.ActionInput.CheckVolume
156            CheckVolume='Yes';
157        end
158        if isfield(Param.ActionInput,'SlidingSequenceLength')
159         nbaver_init=Param.ActionInput.SlidingSequenceLength;
160        end
161        if isfield(Param.ActionInput,'BrightnessRankThreshold')
162          BrightnessRankThreshold=Param.ActionInput.BrightnessRankThreshold;
163        end
164        if isfield(Param.ActionInput,'CheckSubmedian') && Param.ActionInput.CheckSubmedian
165        CheckSubmedian='Yes';
166        end
167        if isfield(Param.ActionInput,'SaturationCoeff')
168            SaturationCoeff=Param.ActionInput.SaturationCoeff;
169        end
170    end   
171    prompt = {'volume scan mode (Yes/No)';...
172        'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';...
173        'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles';...
174        'set to 0 image levels below median(Yes/No)';...
175        'image rescaling coefficient(=2 to reduce the influence of bright particles), =0 for no rescaling' };
176    dlg_title = 'get (slice by slice) a sliding background and substract to each image';
177    num_lines= 5;
178    def     = { CheckVolume;num2str(nbaver_init);num2str(BrightnessRankThreshold);CheckSubmedian;num2str(SaturationCoeff)};
179    answer = inputdlg(prompt,dlg_title,num_lines,def);
180    if isempty(answer)
181        return
182    end
183    %check input consistency
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']);
186        if ~strcmp(check,'Yes')
187            return
188        end
189    end
190    if strcmp(answer{1},'Yes')
191        step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume ;ode
192        ParamOut.NbSlice=1; %nbre of slices displayed
193    else
194        step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
195    end
196    nbaver_ima=str2double(answer{2});%number of images for the sliding background
197    nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
198    if isequal(mod(nbaver,2),0)% if nbaver is even
199        nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
200    end
201    nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver
202    ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes');
203    ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima;
204    ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3});
205    ParamOut.ActionInput.CheckSubmedian=strcmp(answer{4},'Yes');
206    ParamOut.ActionInput.SaturationCoeff=str2double(answer{5});
207    % apply the image rescaling function 'level' (avoid the blinking effects of bright particles)
208%     answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background');
209%     ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes');
210    return
211end
212%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%%
213
214%% read input parameters from an xml file if input is a file name (batch mode)
215checkrun=1;
216RUNHandle=[];
217WaitbarHandle=[];
218if ischar(Param)
219    Param=xml2struct(Param);% read Param as input file (batch case)
220    checkrun=0;
221else
222hseries=findobj(allchild(0),'Tag','series');
223RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
224WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
225end
226
227%% input preparation
228NbSlice_i=Param.IndexRange.NbSlice;
229if ~isequal(NbSlice_i,1)
230    display(['multi-level splitting into ' num2str(NbSlice_i) ' slices']);
231end
232RootPath=Param.InputTable(:,1);
233RootFile=Param.InputTable(:,3);
234SubDir=Param.InputTable(:,2);
235NomType=Param.InputTable(:,4);
236FileExt=Param.InputTable(:,5);
237%hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
238[filecell,i1_series,i2_series,j1_series]=get_file_series(Param);
239% if ~isempty(hdisp),delete(hdisp),end;
240%%%%%%%%%%%%
241    % The cell array filecell is the list of input file names, while
242    % filecell{iview,fileindex}:
243    %        iview: line in the table corresponding to a given file series
244    %        fileindex: file index within  the file series,
245    % 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
246    % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
247%%%%%%%%%%%%
248[FileInfo{1},MovieObject{1}]=get_file_info(filecell{1,1});
249FileType{1}=FileInfo{1}.FileType;
250    if ~isempty(j1_series{1})
251        frame_index{1}=j1_series{1};
252    else
253        frame_index{1}=i1_series{1};
254    end
255
256
257%% output file naming
258FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image'
259if strcmp(FileInfo{1}.FileType,'image')
260    NomTypeOut=NomType{1};
261% if strcmp(lower(NomType{1}(end)),'a')
262%     NomTypeOut=NomType{1};%case of letter appendix
263elseif isempty(j1_series{1})
264    NomTypeOut='_1';
265else
266    NomTypeOut='_1_1';% caseof purely numerical indexing
267end
268OutputDir=[Param.OutputSubDir Param.OutputDirExt];
269
270%% file index parameters
271% NbSlice_i: nbre of slices for i index: different of of 1 for multi-level,
272% the function sub_background is then relaunched by the GUI series for each
273%      slice, incrementing the first index i by 1
274% NbSlice_j: nbre of slices in volume mode
275% nbfield : total number of images treated per slice
276% step: shift of image index at each step of the sliding background (corresponding to the nbre of images in a burst)
277% nbaver_ima: nbre of the images in the sliding sequence used for the background
278% nbaver=nbaver_ima/step: nbre of bursts corresponding to nbaver_ima images. It has been adjusted so that nbaver is an odd integer
279nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
280nbfield_i=size(i1_series{1},2); %nb of fields for the i index
281
282if Param.ActionInput.CheckVolume
283    step=2;% we assume the burst contains only one image pair
284    NbSlice_j=nbfield_j;
285    NbSlice=nbfield_j;
286    nbfield_series=nbfield_i;
287else
288    step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
289        NbSlice_j=1;
290        NbSlice=NbSlice_i;
291    %nbfield_i=floor(nbfield_i/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
292    %nbfield=nbfield_i*NbSlice_i; %total number of fields after adjustement
293    nbfield_series=nbfield_i*nbfield_j;
294end
295nbfield=nbfield_j*nbfield_i; %total number of fields
296nbaver_ima=Param.ActionInput.SlidingSequenceLength;%number of images for the sliding background
297nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
298if isequal(mod(nbaver,2),0)
299    nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
300end
301nbaver_ima=nbaver*step;
302if nbaver_ima > nbfield
303    display('number of images in a slice smaller than the proposed number of images for the sliding average')
304    return
305end
306halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background
307
308%% calculate absolute brightness rank
309rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima);
310if rank==0
311    rank=1;%rank selected in the sorted image series
312end
313
314%% prealocate memory for the sliding background
315try
316    Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1));
317    [npy,npx,nbcolor]=size(Afirst);% the argument nbcolor is important to get npx right for color images
318    if strcmp(class(Afirst),'uint8') % case of 8bit images
319        Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
320        Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
321    else
322        Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
323        Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
324    end
325catch ME
326    msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message])
327    return
328end
329
330
331%%%%%%%  LOOP ON SLICES FOR VOLUME SCAN %%%%%%%
332for j_slice=1:NbSlice_j
333    %% select the series of i indices to process
334    indselect=j_slice:step*NbSlice_j:nbfield;% select file indices of the slice
335    for ifield=1:step-1
336        indselect=[indselect;indselect(end,:)+NbSlice_j];
337    end
338   
339    %% read the first series of nbaver_ima images and sort by luminosity at each pixel
340    for ifield = 1:nbaver_ima
341        ifile=indselect(ifield);
342        filename=filecell{1,ifile};
343        Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
344        if ndims(Aread)==3;%color images
345            Aread=sum(double(Aread),3);% take the sum of color components
346        end
347        Ak(:,:,ifield)=Aread;
348    end
349    Asort=sort(Ak,3);%sort the luminosity of images at each point
350    B=Asort(:,:,rank);%background image
351   
352    %% substract the first background image to the first images
353    display( 'first background image will be substracted')
354    for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image
355        Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
356        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
357        ifile=indselect(ifield);
358        j1=1;
359        if ~isempty(j1_series{1})
360            j1=j1_series{1}(ifile);
361        end
362        newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
363       
364        %write result file
365        if ~isequal(Param.ActionInput.SaturationCoeff,0)
366            C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff);
367            imwrite(C,newname,'BitDepth',16); % save the new image
368        else
369            if ~isfield(FileInfo{1},'BitDepth')
370                FileInfo{1}.BitDepth=16;
371            end
372            if isequal(FileInfo{1}.BitDepth,16)
373                C=uint16(Acor);
374                imwrite(C,newname,'BitDepth',16); % save the new image
375            else
376                C=uint8(Acor);
377                imwrite(C,newname,'BitDepth',8); % save the new image
378            end
379        end
380        display([newname ' written'])
381    end
382   
383    %% repeat the operation on a sliding series of images
384    display('sliding background image will be substracted')
385    if nbfield_series > nbaver_ima
386        for ifield = step*(halfnbaver+1):step:nbfield_series-step*(halfnbaver+1)% ifield +iburst=index of the current processed image
387            update_waitbar(WaitbarHandle,ifield/nbfield_series)
388            if  ~isempty(RUNHandle)&&~strcmp(get(RUNHandle,'BusyAction'),'queue')
389                disp('program stopped by user')
390                return
391            end
392            if nbaver_ima>step
393            Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
394            end
395            %incorporate next burst in the current image series
396            for iburst=1:step
397                ifile=indselect(ifield+iburst+step*halfnbaver);
398                j1=1;
399                if ~isempty(j1_series{1})
400                    j1=j1_series{1}(ifile);
401                end
402                filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
403                Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
404                if ndims(Aread)==3;%color images
405                    Aread=sum(double(Aread),3);% take the sum of color components
406                end
407                Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image
408            end
409            Asort=sort(Ak,3);%sort the new current image series by luminosity
410            B=Asort(:,:,rank);%current background image
411            %substract the background for the current burst
412            for iburst=1:step
413                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
414                Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
415                ifile=indselect(ifield+iburst);
416                if ~isempty(j1_series{1})
417                    j1=j1_series{1}(ifile);
418                end
419                newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
420                %write result file
421                if ~isequal(Param.ActionInput.SaturationCoeff,0)
422                    C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff);
423                    imwrite(C,newname,'BitDepth',16); % save the new image
424                else
425                    if isequal(FileInfo{1}.BitDepth,16)
426                        C=uint16(Acor);
427                        imwrite(C,newname,'BitDepth',16); % save the new image
428                    else
429                        C=uint8(Acor);
430                        imwrite(C,newname,'BitDepth',8); % save the new image
431                    end
432                end
433                display([newname ' written'])
434            end
435        end
436    end
437   
438    %% substract the background from the last images
439    display('last background image will be substracted')
440    for  ifield=nbfield_series-step*halfnbaver+1:nbfield_series
441        Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B);
442        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
443        ifile=indselect(ifield);
444        if ~isempty(j1_series{1})
445            j1=j1_series{1}(ifile);
446        end
447        newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
448        %write result file
449        if ~isequal(Param.ActionInput.SaturationCoeff,0)
450            C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff);
451            imwrite(C,newname,'BitDepth',16); % save the new image
452        else
453            if isequal(FileInfo{1}.BitDepth,16)
454                C=uint16(Acor);
455                imwrite(C,newname,'BitDepth',16); % save the new image
456            else
457                C=uint8(Acor);
458                imwrite(C,newname,'BitDepth',8); % save the new image
459            end
460        end
461        display([newname ' written'])
462    end
463end
464
465function C=levels(A,CheckSubmedian,Coeff)
466
467nblock_y=100;%2*Param.TransformInput.BlockSize;
468nblock_x=100;%2*Param.TransformInput.BlockSize;
469[npy,npx]=size(A);
470[X,Y]=meshgrid(1:npx,1:npy);
471
472%Backg=zeros(size(A));
473%Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
474%Amin=A.*Aflagmin;%values of A at local minima
475% local background: find all the local minima in image subblocks
476if CheckSubmedian
477    fctblock= inline('median(x(:))');
478    Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in  blocks
479    %B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
480    A=A-imresize(Backg,size(A),'bilinear');% substract background interpolated to the initial size image
481end
482fctblock= inline('mean(x(:))');
483AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
484fctblock= inline('var(x(:))');
485AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
486Avalue=AVar./AMean;% typical value of particle luminosity
487Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image
488C=uint16(1000*tanh(A./(Coeff*Avalue)));
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