source: trunk/src/series/sub_background.m @ 854

Last change on this file since 854 was 854, checked in by sommeria, 6 years ago

bugrepair

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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 2008-2014, LEGI UMR 5519 / CNRS UJF 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'; %nbre of slices ('off' by default)
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=[];
89    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
90    last_j=[];
91    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_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    ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
110    FileInfo=get_file_info(FirstFileName);
111    FileType=FileInfo.FileType;
112    CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions), 1));% =1 for images
113    if ~CheckImage
114        msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not an image'])
115        return
116    end
117   
118    %% numbers of fields
119    NbSlice=1;%default
120    if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
121        NbSlice=Param.IndexRange.NbSlice;
122    end
123    incr_j=1;%default
124    if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j)
125        incr_j=Param.IndexRange.incr_j;
126    end
127    if isempty(first_j)||isempty(last_j)
128        nbfield_j=1;
129    else
130        nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices)
131    end
132    incr_i=1;%default
133    first_i=1;last_i=1;incr_i;%default
134    if isfield(Param.IndexRange,'first_i'); last_i=Param.IndexRange.first_i; end   
135    if isfield(Param.IndexRange,'last_i'); last_i=Param.IndexRange.last_i; end
136    if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i)
137        incr_i=Param.IndexRange.incr_i;
138    end
139    nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices)
140    nbfield=nbfield_j*nbfield_i; %total number of fields
141    nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
142   
143    %% setting of  parameters specific to sub_background
144    nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts 
145    if nbfield_i~=1
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   
153    prompt = {'volume scan mode (Yes/No)';'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';...
154        'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'};
155    dlg_title = 'get (slice by slice) a sliding background and substract to each image';
156    num_lines= 3;
157    def     = { 'No';num2str(nbaver_init);'0.1'};
158    answer = inputdlg(prompt,dlg_title,num_lines,def);
159   
160    %check input consistency
161    if strcmp(answer{1},'No') && ~isequal(NbSlice,1)
162        check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice) ' slices']);
163        if ~strcmp(check,'Yes')
164            return
165        end
166    end
167    if strcmp(answer{1},'Yes')
168        step=1;
169    else
170        step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
171    end
172    nbaver_ima=str2double(answer{2});%number of images for the sliding background
173    nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
174    if isequal(mod(nbaver,2),0)% if nbaver is even
175        nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
176    end
177    nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver
178    ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes');
179    ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima;
180    ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3});
181   
182    % apply the image rescaling function 'level' (avoid the blinking effects of bright particles)
183    answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background');
184    ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes');
185    return
186end
187%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%%
188
189%% read input parameters from an xml file if input is a file name (batch mode)
190checkrun=1;
191if ischar(Param)
192    Param=xml2struct(Param);% read Param as input file (batch case)
193    checkrun=0;
194end
195hseries=findobj(allchild(0),'Tag','series');
196RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
197WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
198
199%% input preparation
200NbSlice=Param.IndexRange.NbSlice;
201if ~isequal(NbSlice,1)
202    display(['multi-level splitting into ' num2str(NbSlice) ' slices']);
203end
204RootPath=Param.InputTable(:,1);
205RootFile=Param.InputTable(:,3);
206SubDir=Param.InputTable(:,2);
207NomType=Param.InputTable(:,4);
208FileExt=Param.InputTable(:,5);
209hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
210[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
211if ~isempty(hdisp),delete(hdisp),end;
212%%%%%%%%%%%%
213    % The cell array filecell is the list of input file names, while
214    % filecell{iview,fileindex}:
215    %        iview: line in the table corresponding to a given file series
216    %        fileindex: file index within  the file series,
217    % 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
218    % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
219%%%%%%%%%%%%
220[FileInfo{1},MovieObject{1}]=get_file_info(filecell{1,1});
221FileType{1}=FileInfo{1}.FileType;
222    if ~isempty(j1_series{1})
223        frame_index{1}=j1_series{1};
224    else
225        frame_index{1}=i1_series{1};
226    end
227nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
228nbfield_i=size(i1_series{1},2); %nb of fields for the i index
229nbfield=nbfield_j*nbfield_i; %total number of fields
230nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
231nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
232
233%% output
234FileExtOut='.png'; % write result as .png images for image inputs
235if strcmp(lower(NomType{1}(end)),'a')
236    NomTypeOut=NomType{1};%case of letter appendix
237elseif isempty(j1_series{1})
238    NomTypeOut='_1';
239else
240    NomTypeOut='_1_1';% caseof purely numerical indexing
241end
242
243OutputDir=[Param.OutputSubDir Param.OutputDirExt];
244
245if isequal(Param.ActionInput.CheckVolume,1)
246    step=1;
247else
248    step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
249end
250nbaver_ima=Param.ActionInput.SlidingSequenceLength;%number of images for the sliding background
251nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
252if isequal(mod(nbaver,2),0)
253    nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
254end
255nbaver_ima=nbaver*step;
256if nbaver_ima > nbfield
257    display('number of images in a slice smaller than the proposed number of images for the sliding average')
258    return
259end
260
261% calculate absolute brightness rank
262rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima);
263if rank==0
264    rank=1;%rank selected in the sorted image series
265end
266
267%% prealocate memory for the sliding background
268try
269    Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1));
270    [npy,npx,nbcolor]=size(Afirst);% the argument nbcolor is important to get npx right for color images
271    if strcmp(class(Afirst),'uint8') % case of 8bit images
272        Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
273        Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
274    else
275        Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
276        Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
277    end
278catch ME
279    msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message])
280    return
281end
282
283%% summary of the parameters:
284% nbfield : total number of images treated (in case of multislices the function sub_background is repeated for each slice)
285% step: shift at each step of the sliding background (corresponding to the nbre of images in a burst)
286% nbaver_ima: length of the sequence used for the sliding background
287
288% nbaver=nbaver_ima/step: nbaver_ima has been adjusted so that nbaver is an odd integer
289halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background
290
291%% select the series of image indices to process
292indselect=1:step:nbfield;% select file indices of the slice
293for ifield=1:step-1
294    indselect=[indselect;indselect(end,:)+1];
295end
296
297%% read the first series of nbaver_ima images and sort by luminosity at each pixel
298for ifield = 1:nbaver_ima
299    ifile=indselect(ifield);
300    filename=filecell{1,ifile};
301    Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
302    if ndims(Aread)==3;%color images
303        Aread=sum(double(Aread),3);% take the sum of color components
304    end
305    Ak(:,:,ifield)=Aread;
306end
307Asort=sort(Ak,3);%sort the luminosity of images at each point
308B=Asort(:,:,rank);%background image
309
310%% substract the first background image to the first images
311display( 'first background image will be substracted')
312for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image
313    Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
314    Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
315    ifile=indselect(ifield);
316    j1=1;
317    if ~isempty(j1_series{1})
318        j1=j1_series{1}(ifile);
319    end
320    newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
321   
322    %write result file
323    if Param.ActionInput.CheckLevelTransform
324        C=levels(Acor);
325        imwrite(C,newname,'BitDepth',8); % save the new image
326    else
327        if isequal(FileInfo{1}.BitDepth,16)
328            C=uint16(Acor);
329            imwrite(C,newname,'BitDepth',16); % save the new image
330        else
331            C=uint8(Acor);
332            imwrite(C,newname,'BitDepth',8); % save the new image
333        end
334    end
335    display([newname ' written'])
336end
337
338%% repeat the operation on a sliding series of images
339display('sliding background image will be substracted')
340if nbfield_i > nbaver_ima
341    for ifield = step*(halfnbaver+1):step:nbfield_i-step*(halfnbaver+1)% ifield +iburst=index of the current processed image
342        update_waitbar(WaitbarHandle,ifield/nbfield_i)
343        if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
344            disp('program stopped by user')
345            return
346        end
347        Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
348        %incorporate next burst in the current image series
349        for iburst=1:step
350            ifile=indselect(ifield+iburst+step*halfnbaver);
351            j1=1;
352    if ~isempty(j1_series{1})
353        j1=j1_series{1}(ifile);
354    end
355            filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
356            Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile));
357            if ndims(Aread)==3;%color images
358                Aread=sum(double(Aread),3);% take the sum of color components
359            end
360            Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image
361        end
362        Asort=sort(Ak,3);%sort the new current image series by luminosity
363        B=Asort(:,:,rank);%current background image
364        %substract the background for the current burst
365        for iburst=1:step
366            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
367            Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
368            ifile=indselect(ifield+iburst);
369            if ~isempty(j1_series{1})
370                j1=j1_series{1}(ifile);
371            end
372            newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
373            %write result file
374            if Param.ActionInput.CheckLevelTransform
375                C=levels(Acor);
376                imwrite(C,newname,'BitDepth',8); % save the new image
377            else
378                if isequal(FileInfo{1}.BitDepth,16)
379                    C=uint16(Acor);
380                    imwrite(C,newname,'BitDepth',16); % save the new image
381                else
382                    C=uint8(Acor);
383                    imwrite(C,newname,'BitDepth',8); % save the new image
384                end
385            end
386            display([newname ' written'])       
387        end
388    end
389end
390
391%% substract the background from the last images
392display('last background image will be substracted')
393for  ifield=nbfield_i-step*halfnbaver+1:nbfield_i
394    Acor=double(Ak(:,:,ifield-nbfield_i+step*(2*halfnbaver+1)))-double(B);
395    Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
396    ifile=indselect(ifield);
397    if ~isempty(j1_series{1})
398        j1=j1_series{1}(ifile);
399    end
400    newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); 
401    %write result file
402    if Param.ActionInput.CheckLevelTransform
403        C=levels(Acor);
404        imwrite(C,newname,'BitDepth',8); % save the new image
405    else
406        if isequal(FileInfo{1}.BitDepth,16)
407            C=uint16(Acor);
408            imwrite(C,newname,'BitDepth',16); % save the new image
409        else
410            C=uint8(Acor);
411            imwrite(C,newname,'BitDepth',8); % save the new image
412        end
413    end
414    display([newname ' written'])
415end
416
417
418
419function C=levels(A)
420%whos A;
421B=double(A(:,:,1));
422windowsize=round(min(size(B,1),size(B,2))/20);
423windowsize=floor(windowsize/2)*2+1;
424ix=1/2-windowsize/2:-1/2+windowsize/2;%
425%del=np/3;
426%fct=exp(-(ix/del).^2);
427fct2=cos(ix/(windowsize-1)/2*pi/2);
428%Mfiltre=(ones(5,5)/5^2);
429%Mfiltre=fct2';
430Mfiltre=fct2'*fct2;
431Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
432
433C=filter2(Mfiltre,B);
434C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
435C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
436C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
437C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
438C=tanh(B./(2*C));
439[n,c]=hist(reshape(C,1,[]),100);
440% figure;plot(c,n);
441
442[m,i]=max(n);
443c_max=c(i);
444[dummy,index]=sort(abs(c-c(i)));
445n=n(index);
446c=c(index);
447i_select = find(cumsum(n)<0.95*sum(n));
448if isempty(i_select)
449    i_select = 1:length(c);
450end
451c_select=c(i_select);
452n_select=n(i_select);
453cmin=min(c_select);
454cmax=max(c_select);
455C=(C-cmin)/(cmax-cmin)*256;
456C=uint8(C);
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