source: trunk/src/series/sub_background.m @ 1053

Last change on this file since 1053 was 1033, checked in by sommeria, 6 years ago

miscellaneous updates

File size: 22.6 KB
1%'sub_background': substract a sliding background to an image series
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)
15% function GUI_config=sub_background(Param)
17%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
20% ParamOut: sets options in the GUI series.fig needed for the function
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
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
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)
54% Copyright 2008-2018, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
56%   Joel.Sommeria - Joel.Sommeria (A)
58%     This file is part of the toolbox UVMAT.
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.
65%     UVMAT is distributed in the hope that it will be useful,
66%     but WITHOUT ANY WARRANTY; without even the implied warranty of
68%     GNU General Public License (see LICENSE.txt) for more details.
71function ParamOut=sub_background (Param)
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
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
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
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)
141    %% setting of  parameters specific to sub_background
142    nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts 
143    if nbfield_i~=1
144        nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background,
145        if isequal(mod(nbaver,2),0)% if nbaver is even
146            nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined)
147        end
148        nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts
149    end
151    prompt = {'volume scan mode (Yes/No)';...
152        'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';...
153        'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles';...
154        'set to 0 image levels below median(Yes/No)';...
155        'image rescaling coefficient(high values reduce the influence of bright particles), =0 for no rescaling' };
156    dlg_title = 'get (slice by slice) a sliding background and substract to each image';
157    num_lines= 5;
158    def     = { 'No';num2str(nbaver_init);'0.1';'No';'2'};
159    answer = inputdlg(prompt,dlg_title,num_lines,def);
160    if isempty(answer)
161        return
162    end
163    %check input consistency
164    if strcmp(answer{1},'No') && ~isequal(NbSlice_i,1)
165        check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice_i) ' slices']);
166        if ~strcmp(check,'Yes')
167            return
168        end
169    end
170    if strcmp(answer{1},'Yes')
171        step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume ;ode
172        ParamOut.NbSlice=1; %nbre of slices displayed
173    else
174        step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
175    end
176    nbaver_ima=str2double(answer{2});%number of images for the sliding background
177    nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
178    if isequal(mod(nbaver,2),0)% if nbaver is even
179        nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
180    end
181    nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver
182    ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes');
183    ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima;
184    ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3});
185    ParamOut.ActionInput.CheckSubmedian=strcmp(answer{4},'Yes');
186    ParamOut.ActionInput.SaturationCoeff=str2double(answer{5});
187    % apply the image rescaling function 'level' (avoid the blinking effects of bright particles)
188%     answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background');
189%     ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes');
190    return
192%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%%
194%% read input parameters from an xml file if input is a file name (batch mode)
198if ischar(Param)
199    Param=xml2struct(Param);% read Param as input file (batch case)
200    checkrun=0;
203RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
204WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
207%% input preparation
209if ~isequal(NbSlice_i,1)
210    display(['multi-level splitting into ' num2str(NbSlice_i) ' slices']);
217%hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
219% if ~isempty(hdisp),delete(hdisp),end;
221    % The cell array filecell is the list of input file names, while
222    % filecell{iview,fileindex}:
223    %        iview: line in the table corresponding to a given file series
224    %        fileindex: file index within  the file series,
225    % 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
226    % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
230    if ~isempty(j1_series{1})
231        frame_index{1}=j1_series{1};
232    else
233        frame_index{1}=i1_series{1};
234    end
237%% output file naming
238FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image'
239if strcmp(FileInfo{1}.FileType,'image')
240    NomTypeOut=NomType{1};
241% if strcmp(lower(NomType{1}(end)),'a')
242%     NomTypeOut=NomType{1};%case of letter appendix
243elseif isempty(j1_series{1})
244    NomTypeOut='_1';
246    NomTypeOut='_1_1';% caseof purely numerical indexing
248OutputDir=[Param.OutputSubDir Param.OutputDirExt];
250%% file index parameters
251% NbSlice_i: nbre of slices for i index: different of of 1 for multi-level,
252% the function sub_background is then relaunched by the GUI series for each
253%      slice, incrementing the first index i by 1
254% NbSlice_j: nbre of slices in volume mode
255% nbfield : total number of images treated per slice
256% step: shift of image index at each step of the sliding background (corresponding to the nbre of images in a burst)
257% nbaver_ima: nbre of the images in the sliding sequence used for the background
258% nbaver=nbaver_ima/step: nbre of bursts corresponding to nbaver_ima images. It has been adjusted so that nbaver is an odd integer
259nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
260nbfield_i=size(i1_series{1},2); %nb of fields for the i index
262if Param.ActionInput.CheckVolume
263    step=2;% we assume the burst contains only one image pair
264    NbSlice_j=nbfield_j;
265    NbSlice=nbfield_j;
266    nbfield_series=nbfield_i;
268    step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
269        NbSlice_j=1;
270        NbSlice=NbSlice_i;
271    %nbfield_i=floor(nbfield_i/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
272    %nbfield=nbfield_i*NbSlice_i; %total number of fields after adjustement
273    nbfield_series=nbfield_i*nbfield_j;
275nbfield=nbfield_j*nbfield_i; %total number of fields
276nbaver_ima=Param.ActionInput.SlidingSequenceLength;%number of images for the sliding background
277nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
278if isequal(mod(nbaver,2),0)
279    nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
282if nbaver_ima > nbfield
283    display('number of images in a slice smaller than the proposed number of images for the sliding average')
284    return
286halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background
288%% calculate absolute brightness rank
290if rank==0
291    rank=1;%rank selected in the sorted image series
294%% prealocate memory for the sliding background
296    Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1));
297    [npy,npx,nbcolor]=size(Afirst);% the argument nbcolor is important to get npx right for color images
298    if strcmp(class(Afirst),'uint8') % case of 8bit images
299        Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
300        Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
301    else
302        Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
303        Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
304    end
305catch ME
306    msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message])
307    return
311%%%%%%%  LOOP ON SLICES FOR VOLUME SCAN %%%%%%%
312for j_slice=1:NbSlice_j
313    %% select the series of i indices to process
314    indselect=j_slice:step*NbSlice_j:nbfield;% select file indices of the slice
315    for ifield=1:step-1
316        indselect=[indselect;indselect(end,:)+NbSlice_j];
317    end
319    %% read the first series of nbaver_ima images and sort by luminosity at each pixel
320    for ifield = 1:nbaver_ima
321        ifile=indselect(ifield);
322        filename=filecell{1,ifile};
323        Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
324        if ndims(Aread)==3;%color images
325            Aread=sum(double(Aread),3);% take the sum of color components
326        end
327        Ak(:,:,ifield)=Aread;
328    end
329    Asort=sort(Ak,3);%sort the luminosity of images at each point
330    B=Asort(:,:,rank);%background image
332    %% substract the first background image to the first images
333    display( 'first background image will be substracted')
334    for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image
335        Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
336        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
337        ifile=indselect(ifield);
338        j1=1;
339        if ~isempty(j1_series{1})
340            j1=j1_series{1}(ifile);
341        end
342        newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
344        %write result file
345        if ~isequal(Param.ActionInput.SaturationCoeff,0)
346            C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff);
347            imwrite(C,newname,'BitDepth',16); % save the new image
348        else
349            if ~isfield(FileInfo{1},'BitDepth')
350                FileInfo{1}.BitDepth=16;
351            end
352            if isequal(FileInfo{1}.BitDepth,16)
353                C=uint16(Acor);
354                imwrite(C,newname,'BitDepth',16); % save the new image
355            else
356                C=uint8(Acor);
357                imwrite(C,newname,'BitDepth',8); % save the new image
358            end
359        end
360        display([newname ' written'])
361    end
363    %% repeat the operation on a sliding series of images
364    display('sliding background image will be substracted')
365    if nbfield_series > nbaver_ima
366        for ifield = step*(halfnbaver+1):step:nbfield_series-step*(halfnbaver+1)% ifield +iburst=index of the current processed image
367            update_waitbar(WaitbarHandle,ifield/nbfield_series)
368            if  ~isempty(RUNHandle)&&~strcmp(get(RUNHandle,'BusyAction'),'queue')
369                disp('program stopped by user')
370                return
371            end
372            if nbaver_ima>step
373            Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
374            end
375            %incorporate next burst in the current image series
376            for iburst=1:step
377                ifile=indselect(ifield+iburst+step*halfnbaver);
378                j1=1;
379                if ~isempty(j1_series{1})
380                    j1=j1_series{1}(ifile);
381                end
382                filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
383                Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
384                if ndims(Aread)==3;%color images
385                    Aread=sum(double(Aread),3);% take the sum of color components
386                end
387                Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image
388            end
389            Asort=sort(Ak,3);%sort the new current image series by luminosity
390            B=Asort(:,:,rank);%current background image
391            %substract the background for the current burst
392            for iburst=1:step
393                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
394                Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
395                ifile=indselect(ifield+iburst);
396                if ~isempty(j1_series{1})
397                    j1=j1_series{1}(ifile);
398                end
399                newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
400                %write result file
401                if ~isequal(Param.ActionInput.SaturationCoeff,0)
402                    C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff);
403                    imwrite(C,newname,'BitDepth',16); % save the new image
404                else
405                    if isequal(FileInfo{1}.BitDepth,16)
406                        C=uint16(Acor);
407                        imwrite(C,newname,'BitDepth',16); % save the new image
408                    else
409                        C=uint8(Acor);
410                        imwrite(C,newname,'BitDepth',8); % save the new image
411                    end
412                end
413                display([newname ' written'])
414            end
415        end
416    end
418    %% substract the background from the last images
419    display('last background image will be substracted')
420    for  ifield=nbfield_series-step*halfnbaver+1:nbfield_series
421        Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B);
422        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
423        ifile=indselect(ifield);
424        if ~isempty(j1_series{1})
425            j1=j1_series{1}(ifile);
426        end
427        newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
428        %write result file
429        if ~isequal(Param.ActionInput.SaturationCoeff,0)
430            C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff);
431            imwrite(C,newname,'BitDepth',16); % save the new image
432        else
433            if isequal(FileInfo{1}.BitDepth,16)
434                C=uint16(Acor);
435                imwrite(C,newname,'BitDepth',16); % save the new image
436            else
437                C=uint8(Acor);
438                imwrite(C,newname,'BitDepth',8); % save the new image
439            end
440        end
441        display([newname ' written'])
442    end
445function C=levels(A,CheckSubmedian,Coeff)
453%Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
454%Amin=A.*Aflagmin;%values of A at local minima
455% local background: find all the local minima in image subblocks
456if CheckSubmedian
457    fctblock= inline('median(x(:))');
458    Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in  blocks
459    %B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
460    A=A-imresize(Backg,size(A),'bilinear');% substract background interpolated to the initial size image
462fctblock= inline('mean(x(:))');
463AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
464fctblock= inline('var(x(:))');
465AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
466Avalue=AVar./AMean;% typical value of particle luminosity
467Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image
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