source: trunk/src/series/sub_background.m @ 1032

Last change on this file since 1032 was 1032, checked in by sommeria, 6 years ago

reading LaVision? images improved

File size: 22.8 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    ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom','image_DaVis'};%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
118    %% numbers of fields
119    NbSlice_i=1;%default
120    if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
121        NbSlice_i=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    first_i=1;last_i=1;incr_i=1;%default
133    if isfield(Param.IndexRange,'MinIndex_i'); first_i=Param.IndexRange.MinIndex_i; end   
134    if isfield(Param.IndexRange,'MaxIndex_i'); last_i=Param.IndexRange.MaxIndex_i; end
135    if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i)
136        incr_i=Param.IndexRange.incr_i;
137    end
138    nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices)
139    nbfield=nbfield_j*nbfield_i; %total number of fields
140    nbfield_i=floor(nbfield/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
142    %% setting of  parameters specific to sub_background
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
152    prompt = {'volume scan mode (Yes/No)';...
153        '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        'set to 0 image levels below median(Yes/No)';...
156        'image rescaling coefficient(high values reduce the influence of bright particles), =0 for no rescaling' };
157    dlg_title = 'get (slice by slice) a sliding background and substract to each image';
158    num_lines= 5;
159    def     = { 'No';num2str(nbaver_init);'0.1';'No';'2'};
160    answer = inputdlg(prompt,dlg_title,num_lines,def);
161    if isempty(answer)
162        return
163    end
164    %check input consistency
165    if strcmp(answer{1},'No') && ~isequal(NbSlice_i,1)
166        check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice_i) ' slices']);
167        if ~strcmp(check,'Yes')
168            return
169        end
170    end
171    if strcmp(answer{1},'Yes')
172        step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume ;ode
173        ParamOut.NbSlice=1; %nbre of slices displayed
174    else
175        step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
176    end
177    nbaver_ima=str2double(answer{2});%number of images for the sliding background
178    nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
179    if isequal(mod(nbaver,2),0)% if nbaver is even
180        nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
181    end
182    nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver
183    ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes');
184    ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima;
185    ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3});
186    ParamOut.ActionInput.CheckSubmedian=strcmp(answer{4},'Yes');
187    ParamOut.ActionInput.SaturationCoeff=str2double(answer{5});
188    % apply the image rescaling function 'level' (avoid the blinking effects of bright particles)
189%     answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background');
190%     ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes');
191    return
193%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%%
195%% read input parameters from an xml file if input is a file name (batch mode)
199if ischar(Param)
200    Param=xml2struct(Param);% read Param as input file (batch case)
201    checkrun=0;
204RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
205WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
208%% input preparation
210if ~isequal(NbSlice_i,1)
211    display(['multi-level splitting into ' num2str(NbSlice_i) ' slices']);
218%hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
220% if ~isempty(hdisp),delete(hdisp),end;
222    % The cell array filecell is the list of input file names, while
223    % filecell{iview,fileindex}:
224    %        iview: line in the table corresponding to a given file series
225    %        fileindex: file index within  the file series,
226    % 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
227    % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
231    if ~isempty(j1_series{1})
232        frame_index{1}=j1_series{1};
233    else
234        frame_index{1}=i1_series{1};
235    end
238%% output file naming
239FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image'
240if strcmp(FileInfo{1}.FileType,'image')
241    NomTypeOut=NomType{1};
242% if strcmp(lower(NomType{1}(end)),'a')
243%     NomTypeOut=NomType{1};%case of letter appendix
244elseif isempty(j1_series{1})
245    NomTypeOut='_1';
247    NomTypeOut='_1_1';% caseof purely numerical indexing
249OutputDir=[Param.OutputSubDir Param.OutputDirExt];
251%% file index parameters
252% NbSlice_i: nbre of slices for i index: different of of 1 for multi-level,
253% the function sub_background is then relaunched by the GUI series for each
254%      slice, incrementing the first index i by 1
255% NbSlice_j: nbre of slices in volume mode
256% nbfield : total number of images treated per slice
257% step: shift of image index at each step of the sliding background (corresponding to the nbre of images in a burst)
258% nbaver_ima: nbre of the images in the sliding sequence used for the background
259% nbaver=nbaver_ima/step: nbre of bursts corresponding to nbaver_ima images. It has been adjusted so that nbaver is an odd integer
260nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
261nbfield_i=size(i1_series{1},2); %nb of fields for the i index
263if Param.ActionInput.CheckVolume
264    step=2;% we assume the burst contains only one image pair
265    NbSlice_j=nbfield_j;
266    NbSlice=nbfield_j;
267    nbfield_series=nbfield_i;
269    step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
270        NbSlice_j=1;
271        NbSlice=NbSlice_i;
272    %nbfield_i=floor(nbfield_i/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
273    %nbfield=nbfield_i*NbSlice_i; %total number of fields after adjustement
274    nbfield_series=nbfield_i*nbfield_j;
276nbfield=nbfield_j*nbfield_i; %total number of fields
277nbaver_ima=Param.ActionInput.SlidingSequenceLength;%number of images for the sliding background
278nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
279if isequal(mod(nbaver,2),0)
280    nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
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
287halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background
289%% calculate absolute brightness rank
291if rank==0
292    rank=1;%rank selected in the sorted image series
295%% prealocate memory for the sliding background
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
312%%%%%%%  LOOP ON SLICES FOR VOLUME SCAN %%%%%%%
313for j_slice=1:NbSlice_j
314    %% select the series of i indices to process
315    indselect=j_slice:step*NbSlice_j:nbfield;% select file indices of the slice
316    for ifield=1:step-1
317        indselect=[indselect;indselect(end,:)+NbSlice_j];
318    end
320    %% read the first series of nbaver_ima images and sort by luminosity at each pixel
321    for ifield = 1:nbaver_ima
322        ifile=indselect(ifield);
323        filename=filecell{1,ifile};
324        Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
325        if ndims(Aread)==3;%color images
326            Aread=sum(double(Aread),3);% take the sum of color components
327        end
328        Ak(:,:,ifield)=Aread;
329    end
330    Asort=sort(Ak,3);%sort the luminosity of images at each point
331    B=Asort(:,:,rank);%background image
333    %% substract the first background image to the first images
334    display( 'first background image will be substracted')
335    for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image
336        Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
337        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
338        ifile=indselect(ifield);
339        j1=1;
340        if ~isempty(j1_series{1})
341            j1=j1_series{1}(ifile);
342        end
343        newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
345        %write result file
346        if ~isequal(Param.ActionInput.SaturationCoeff,0)
347            C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff);
348            imwrite(C,newname,'BitDepth',16); % save the new image
349        else
350            if ~isfield(FileInfo{1},'BitDepth')
351                FileInfo{1}.BitDepth=16;
352            end
353            if isequal(FileInfo{1}.BitDepth,16)
354                C=uint16(Acor);
355                imwrite(C,newname,'BitDepth',16); % save the new image
356            else
357                C=uint8(Acor);
358                imwrite(C,newname,'BitDepth',8); % save the new image
359            end
360        end
361        display([newname ' written'])
362    end
364    %% repeat the operation on a sliding series of images
365    display('sliding background image will be substracted')
366    if nbfield_series > nbaver_ima
367        for ifield = step*(halfnbaver+1):step:nbfield_series-step*(halfnbaver+1)% ifield +iburst=index of the current processed image
368            update_waitbar(WaitbarHandle,ifield/nbfield_series)
369            if  ~isempty(RUNHandle)&&~strcmp(get(RUNHandle,'BusyAction'),'queue')
370                disp('program stopped by user')
371                return
372            end
373            if nbaver_ima>step
374            Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
375            end
376            %incorporate next burst in the current image series
377            for iburst=1:step
378                ifile=indselect(ifield+iburst+step*halfnbaver);
379                j1=1;
380                if ~isempty(j1_series{1})
381                    j1=j1_series{1}(ifile);
382                end
383                filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
384                Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
385                if ndims(Aread)==3;%color images
386                    Aread=sum(double(Aread),3);% take the sum of color components
387                end
388                Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image
389            end
390            Asort=sort(Ak,3);%sort the new current image series by luminosity
391            B=Asort(:,:,rank);%current background image
392            %substract the background for the current burst
393            for iburst=1:step
394                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
395                Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
396                ifile=indselect(ifield+iburst);
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 ~isequal(Param.ActionInput.SaturationCoeff,0)
403                    C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff);
404                    imwrite(C,newname,'BitDepth',16); % 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'])
415            end
416        end
417    end
419    %% substract the background from the last images
420    display('last background image will be substracted')
421    for  ifield=nbfield_series-step*halfnbaver+1:nbfield_series
422        Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B);
423        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
424        ifile=indselect(ifield);
425        if ~isempty(j1_series{1})
426            j1=j1_series{1}(ifile);
427        end
428        newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
429        %write result file
430        if ~isequal(Param.ActionInput.SaturationCoeff,0)
431            C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff);
432            imwrite(C,newname,'BitDepth',16); % save the new image
433        else
434            if isequal(FileInfo{1}.BitDepth,16)
435                C=uint16(Acor);
436                imwrite(C,newname,'BitDepth',16); % save the new image
437            else
438                C=uint8(Acor);
439                imwrite(C,newname,'BitDepth',8); % save the new image
440            end
441        end
442        display([newname ' written'])
443    end
446function C=levels(A,CheckSubmedian,Coeff)
454%Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
455%Amin=A.*Aflagmin;%values of A at local minima
456% local background: find all the local minima in image subblocks
457if CheckSubmedian
458    fctblock= inline('median(x(:))');
459    Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in  blocks
460    %B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
461    A=A-imresize(Backg,size(A),'bilinear');% substract background interpolated to the initial size image
463fctblock= inline('mean(x(:))');
464AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
465fctblock= inline('var(x(:))');
466AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
467Avalue=AVar./AMean;% typical value of particle luminosity
468Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image
Note: See TracBrowser for help on using the repository browser.